U.S. Fish & Wildlife Service

Stone Lakes

National Wildlife Refuge

Comprehensive Conservation Plan
Disclaimer

CCPs provide long term guidance for management decisions and set forth goals, objectives, 

and strategies needed to accomplish refuge purposes and identify the Service’s best estimate 

of future needs. These plans detail program planning levels that are sometimes substantially 

above current budget allocations and, as such, are primarily for Service strategic planning 

and program prioritization purposes. The plans do not constitute a commitment for staffing 

increases, operational and maintenance increases, or funding for future land acquisition.

Vision Statement

Stone Lakes National Wildlife Refuge belongs to a limited group among the 540 national 

wildlife refuges that protect fish, wildlife, and habitat within an urban area. Through 

collaboration with public and private partners, Stone Lakes conserves and enhances a range 

of scarce Sacramento-San Joaquin Delta and Central Valley habitats and the fish, wildlife, 

and plants they support. It sustains freshwater wetlands, wooded riparian corridors, and 

grasslands that facilitate wildlife movement and compensate for habitat fragmentation. 

Managed wetlands are of sufficient size to maintain abundant wildlife populations. 

Grasslands consist of a sustainable mix of native and desirable nonnative species that 

support a variety of grassland-dependent species. The Refuge reduces further habitat 

fragmentation and buffers the effects of urbanization on agricultural lands and adjacent 

natural areas within the Delta region.

The Refuge pursues a land conservation program that complements other regional efforts 

and initiatives. Management efforts expand and diversify habitats for migratory birds and 

a range of species at risk. The Refuge promotes cooperative farming opportunities and 

strives to maintain traditional agricultural practices in southwestern Sacramento County 

that have proven benefits for migratory birds experiencing declines, such as long-billed 

curlews (Numenius americanus), Swainson’s hawks (Buteo swainsoni) and sandhill cranes 

(Grus canadensis). Through cooperation with other agencies, conservation organizations, 

neighbors, and other partners, the Refuge develops and manages wetlands in a manner 

that reflects historic hydrologic patterns and is consistent with local, State, and Federal 

floodplain management goals and programs. 

Stone Lakes was established as a national wildlife refuge because of passionate support from 

people who recognized its ecological importance and critical role for the floodplain of the 

Beach-Stone Lakes basin.. The community sees the Refuge as a sanctuary for fish, wildlife 

and the habitats upon which they depend, a site for recreation and learning and a natural 

setting that can enrich their lives according to their values. Visitors representing the area’s 

diversity enjoy increasing opportunities for accessible recreation that harmonizes with 

Refuge conservation efforts, such as hunting, fishing, wildlife observation and photography. 

The education community looks to the Refuge as a key partner in environmental education 

programming. Volunteers from all walks of life find an outlet for their interests and talents 

in a responsive and appreciative setting.

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Stone Lakes NWR Comprehensive Conservation Plan

1 Introduction .................................................................................................1

Introduction.................................................................................................................................1

Purpose and Need for the Comprehensive Conservation Plan (CCP)................................1

U.S. Fish and Wildlife Service and National Wildlife Refuge System...............................1

U.S. Fish and Wildlife Service Responsibilities .............................................................1

The National Wildlife Refuge System ..............................................................................2

Legal and Policy Guidance..................................................................................................2

Stone Lakes National Wildlife Refuge ....................................................................................5

Location .......................................................................................................................................5

Refuge Setting .....................................................................................................................5

History of Refuge Establishment and Acquisition .........................................................7

Land Protection ...................................................................................................................7

Land Conservation Methods..............................................................................................8

Partnerships .......................................................................................................................11

Refuge Purposes................................................................................................................13

Related Projects and Studies in the Area .............................................................................13

U.S. Fish and Wildlife Service ........................................................................................13

Other Agencies and Projects............................................................................................14

2 The Planning Process..............................................................................17

The Planning Process...............................................................................................................17

The Stone Lakes CCP Process...............................................................................................17

Issues Identified by the Public ...............................................................................................18

Management.......................................................................................................................18

General Access ...................................................................................................................19

Boating/Waterskiing..........................................................................................................20

Horseback Riding..............................................................................................................20

Fishing.................................................................................................................................20

Hunting ...............................................................................................................................21

Education/Interpretation .................................................................................................22

Wildlife Observation..........................................................................................................22

Other Comments................................................................................................................23

General................................................................................................................................23

3 Refuge Resources.....................................................................................25

Ecoregion Setting.....................................................................................................................25

Flyway Setting...................................................................................................................25

Natural/Historic Conditions.............................................................................................25

Geographic and Physical Setting.....................................................................................26

Topography.........................................................................................................................26

Geology................................................................................................................................26

Soils......................................................................................................................................28

Climate ................................................................................................................................28

Air Quality ..........................................................................................................................28

Contents
ii Stone Lakes NWR Comprehensive Conservation Plan

Contaminants and Water Quality ....................................................................................30

Hydrology...........................................................................................................................34

Water Supply......................................................................................................................35

Biological Resources ................................................................................................................36

Plant Communities ............................................................................................................36

Wildlife ................................................................................................................................40

Special Status Species.......................................................................................................46

Visitor Services .........................................................................................................................50

Ecoregion Scale..................................................................................................................50

Local Scale..........................................................................................................................51

Socioeconomic Resources ........................................................................................................53

Cultural Resources...................................................................................................................54

Cultural Resources ............................................................................................................54

Historic Setting..................................................................................................................54

Archeology..........................................................................................................................55

Land Use....................................................................................................................................56

Wilderness and Other Special Management Areas .............................................................56

Current Management Practices .............................................................................................56

Wetlands..............................................................................................................................56

Mosquito Control ...............................................................................................................58

Riparian...............................................................................................................................58

Grasslands ..........................................................................................................................59

Weed Control......................................................................................................................60

Farming Program..............................................................................................................60

Monitoring and Surveys ...................................................................................................61

4 Challenges .................................................................................................63

Invasive Species........................................................................................................................63

Basin Hydrology and Water Quality......................................................................................64

Floodplain Conditions .......................................................................................................64

Flood Control Projects......................................................................................................65

Water Quality .....................................................................................................................66

Land Use Changes ...................................................................................................................67

Urbanization and Vineyard Conversion..........................................................................67

Other Human Impacts .............................................................................................................67

Air Quality ..........................................................................................................................67

Illegal Activity....................................................................................................................67

Mosquito Management .....................................................................................................68

Avian Bird Flu....................................................................................................................68

5 Refuge Vision, Goals, and Objectives...................................................71

Vision Statement.......................................................................................................................71

Goals............................................................................................................................................72

6 Implementation and Monitoring ............................................................93

Step-Down Management Plans...............................................................................................93

Funding and Staffing ................................................................................................................93

Compliance Requirements.......................................................................................................94

Partnership Opportunities .......................................................................................................94

Adaptive Management .............................................................................................................94

Plan Amendment and Revision...............................................................................................95

References.......................................................................................................99
Stone Lakes NWR Comprehensive Conservation Plan iii

Figures

Figure 1. Ecoregion and Watershed Map .....................................................................................6

Figure 2. Land Status......................................................................................................................9

Figure 3. Core and Cooperative WM Areas ...............................................................................10

Figure 4. Refuge Roads and Units...............................................................................................27

Figure 5. Vegetation Map..............................................................................................................37

Figure 6. Proposed Habitat Management ...................................................................................73

Figure 7. Proposed Visitor Services Management.....................................................................74

Tables

Table 1. Invasive Plant Species Targeted for Control on the Stone Lakes NWR..................64

Table 2. Step-down Management Plans ......................................................................................93

Table 3. Estimated Initial Capital Outlay to Implement the CCP ..........................................96

Table 4. Estimated Annual Cost to Implement the CCP..........................................................97

Appendices....................................................................................................107

Appendix A. Compatibility Determinations ..............................................................................109

Fishing ...................................................................................................................................109

Wildlife Observation and Photography................................................................................114

Environmental Education and Interpretation....................................................................119

High-speed Boating................................................................................................................124

Recreational Boating..............................................................................................................130

Research...................................................................................................................................137

Plant Gathering ......................................................................................................................141

Mosquito Monitoring and Control ........................................................................................145

Grazing ...................................................................................................................................162

Appendix B. FONSI and Environmental Assessment.............................................................171

Appendix C. Wildlife Species Found on Stone Lakes NWR ...................................................221

Appendix D. Fish Species Found on Stone Lakes NWR ........................................................231

Appendix E. Wilderness Review ................................................................................................233

Appendix F. Endangered Species Act, Section 7 Consultation ..............................................235

Appendix G. Response to Comments .........................................................................................277

Appendix H. Plant Species Found on Stone Lakes NWR........................................................381

Appendix I. Glossary ...................................................................................................................393

Appendix J. Summary of Public Involvement/Comments and Consultation/Coordination......401

Appendix K. Preparer List ..........................................................................................................405

Appendix L. Integrated Pest Management Plan for Mosquito-Associated Threats ...........407
iv Stone Lakes NWR Comprehensive Conservation Plan

Acronyms

California Department of Boating and Waterways DBW

California Department of Fish and Game DFG

California Department of Water Resources DWR

California Endangered Species Act CESA

Comprehensive Conservation Plan CCP

California Department of Transportation Caltrans

California Department of Parks and Recreation DPR

California Native Plant Society CNPS

Endangered Species Act ESA

Environmental Assessment EA

Environmental Impact Statement EIS

Global positioning system GPS

Memorandum of Agreement MOA

Memorandum of Understanding MOU

National Wildlife Refuge Refuge

National Wildlife Refuge System Refuge System

National Wildlife Refuge System Improvement Act of 1977 Improvement Act

Natural Resources Conservation Service NRCS

National Environmental Policy Act NEPA

Native American Grave Protection and Repatriation Act NAGPRA

Sacramento-San Joaquin Delta Delta

Stone Lakes National Wildlife Refuge Refuge

Sacramento Regional County Sanitation District SRCSD

State Water Resources Control Board SWRCB

Sacramento Regional Wastewater Treatment Plant SRWTP

Sacramento-Yolo Mosquito and Vector Control District SYMVCD

University of California UC

U.S. Army Corps of Engineers USACE

U.S. Environmental Protection Agency USEPA

U.S. Fish and Wildlife Service Service

U.S. Department of Agriculture USDA

U. S. Geological Survey USGS
Stone Lakes NWR Comprehensive Conservation Plan 

1 Introduction

Introduction

Stone Lakes National Wildlife Refuge 

(Refuge) was established in 1994, becoming 

the 505th refuge in the National Wildlife 

Refuge System (NWRS). The Refuge 

boundary was estimated at 18,212 acres 

when established (USFWS 1992), but 

subsequent surveys have revised the actual 

Refuge boundary to a more accurate figure 

of 17,641 acres. The boundary included a 

core Refuge area of approximately 9,000 

acres and an approximately 9,000 acre 

“Cooperative Wildlife Management Area” 

where the Service first seeks to enter into 

cooperative agreements and memoranda of 

understanding with landowners or purchase 

conservation easements. The Service 

actively manages approximately 6,000 

acres. The Refuge is located in the BeachStone Lakes Basin within the Sacramento 

Valley in southwestern Sacramento County; 

it lies about ten miles south of the city of 

Sacramento, straddling Interstate-5 from 

the town of Freeport south to Lost Slough.

Purpose and Need for the 

Comprehensive Conservation Plan 

(CCP) 

The Service prepared this draft CCP to 

guide management of fish, wildlife, plants, 

other natural resources and visitor use 

on the Refuge for the next 15 years. The 

Comprehensive Conservation Plan (CCP) 

is flexible; it will be revised periodically 

to ensure that its goals, objectives, 

implementation strategies and timetables 

remain valid and appropriate. Major 

revisions require and provide a process 

for public involvement and National 

Environmental Policy Act (NEPA) review, if 

needed.

The NWRS Improvement Act of 1997 

requires that the Service develop a CCP 

for each refuge by 2012, and that refuges 

be managed in a way that ensures the 

long-term conservation of fish, wildlife, 

plants, and their habitats and provides for 

compatible wildlife-dependent recreation. 

The purposes for developing a CCP are to:

• Provide a clear statement of direction for 

the future management

• Provide long-term continuity in Refuge 

Complex management;

• Communicate the U.S. Fish and Wildlife 

Service’s management priorities for the 

Refuges to their conservation partners, 

neighbors, visitors, and the general public;

• Provide an opportunity for the public to 

help shape the future management of the 

Refuges;

• Ensure that management programs on the 

Refuges are consistent with the mandates 

of the National Wildlife Refuge System 

(Refuge System) and the purposes for 

which each Refuge was established;

• Ensure that the management of the 

Refuges fully considers resource priorities 

and management strategies identified in 

other Federal, State, and local plans;

• Provide a basis for budget requests to 

support the Refuge’s needs staffing, 

operations, maintenance, and capital 

improvements; and

• Evaluate existing and proposed uses 

of each refuge to ensure that they are 

compatible with the refuge purpose(s) 

as well as the maintenance of biological 

integrity, diversity, and environmental 

health.

U.S. Fish and Wildlife Service and 

National Wildlife Refuge System

U.S. Fish and Wildlife Service 

Responsibilities 

The U.S. Fish and Wildlife Service (Service) 

is the primary Federal agency responsible 

for conserving and enhancing the nation’s 
 Stone Lakes NWR Comprehensive Conservation Plan

fish and wildlife populations and their 

habitats. Although this responsibility is 

shared with other Federal, State, Tribal, 

local, and private entities, the Service 

has specific responsibilities for migratory 

birds, threatened and endangered species, 

inter-jurisdictional fish and certain marine 

mammals. The Service has similar 

responsibilities for the lands and waters it 

administers to support the conservation and 

enhancement of fish and wildlife.

The National 

Wildlife Refuge 

System

The National 

Wildlife Refuge 

System (NWRS) is 

the largest system 

of lands in the 

world dedicated to 

the conservation 

of fish and wildlife. 

Operated and 

managed by the 

Service, it currently 

includes 545 refuges 

with a combined 

area of more than 

94 million acres. 

The majority of 

refuge lands (over 

77 million acres) are 

located in Alaska. 

The remaining 

acreage is scattered 

across the other 49 

states and several island territories. About 

20.6 million acres are managed as wilderness 

under the Wilderness Act of 1964.

The NWRS started in 1903, when President 

Theodore Roosevelt protected an island with 

nesting pelicans, herons, ibis, and roseate 

spoonbills in Florida’s Indian River from 

feather collectors decimating their colonies. 

He established Pelican Island as the nation’s 

first bird sanctuary and went on to establish 

many other sanctuaries for wildlife during 

his tenure. This small network of sanctuaries 

continued to expand, later becoming the 

NWRS. In contrast to other public lands, 

which are managed for multiple uses, 

refuges are specifically managed for fish and 

wildlife conservation.

The mission of the NWRS, established by 

the NWRS Improvement Act of 1997, 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 goals of the NWRS, as established by 

the Policy in the Service Manual (601 FW 1) 

(July 26, 2006), are to: 

Conserve a diversity of fish, wildlife, 

and plants and their habitats, including 

species that are endangered or 

threatened with becoming endangered.

Develop and maintain a network 

of habitats for migratory birds, 

anadromous and interjurisdictional fish, 

and marine mammal populations that is 

strategically distributed and carefully 

managed to meet important life history 

needs of these species across their 

ranges.

Conserve those ecosystems, plant 

communities, wetlands of national 

or international significance, and 

landscapes and seascapes that 

are unique, rare, declining or 

underrepresented in existing protection 

efforts.

Provide and enhance opportunities 

to participate in compatible wildlifedependent recreation (hunting, fishing, 

wildlife observation and photography, 

and environmental education and 

interpretation).

Foster understanding and instill 

appreciation of the diversity and 

interconnectedness of fish, wildlife, and 

plants and their habitats.

Legal and Policy Guidance 

Legal mandates and Service policies govern 

the Service’s planning and management of 

the NWRS. A list and brief description can 

be found at the “Division of Congressional 

and Legislative Affairs, USFWS” Web 

site (http://laws.fws.gov). In addition, 

•

•

•

•

•

The Service 

has specific 

responsibilities for 

migratory birds 

such as this great 

egret. 

Photo by Tom Harvey, 

USFWS
Stone Lakes NWR Comprehensive Conservation Plan 

the Service has developed draft or final 

policies to guide NWRS planning and 

management. These policies can be found at 

the “NWRS Policies” Web site (http://www.

fws.gov/refuges/policymakers/nwrpolicies.

html). The main sources of legal and policy 

guidance for the CCP and EA are described 

below. 

National Wildlife Refuge System 

Improvement Act of 1997

Statutory authority for Service management 

and associated habitat management 

planning on units of the NWRS is derived 

from the National Wildlife Refuge System 

Administration Act of 1966 (Refuge 

Administration Act), which was significantly 

amended by the National Wildlife Refuge 

System Improvement Act of 1997 (Refuge 

Improvement Act, 16 U.S.C. 668dd-668ee). 

Section 4(a)(3) of the Refuge Improvement 

Act states, “With respect to the National 

Wildlife System [NWRS], it is the policy 

of the United States that – (A) each refuge 

shall be managed to fulfill the mission of the 

System, as well as the specific purposes for 

which that refuge was established...” The 

Refuge Improvement Act also states that 

the “...purposes of the refuge and purposes 

for each refuge mean the purposes specified 

in or derived from law, proclamation, 

executive order, agreement, public land 

order, donation document, or administrative 

memorandum establishing, authorizing, or 

expanding a refuge, refuge unit, or refuge 

subunit.” 

The Refuge Administration Act, as amended, 

clearly establishes wildlife conservation as 

the core NWRS mission. House Report 105-

106, accompanying the Refuge Improvement 

Act, states “...the fundamental mission of 

our System is wildlife conservation...wildlife 

and wildlife conservation must come first.” 

In contrast to some other systems of federal 

lands which are managed on a sustainedyield basis for multiple uses, the NWRS 

is a primary-use network of lands and 

waters. First and foremost, refuges are 

managed for fish, wildlife, plants, and their 

habitats. In addition, units of the NWRS 

are legally closed to all public access and 

use, including economic uses, unless and 

until they are officially opened through an 

analytical, public process called the refuge 

compatibility process. With the exception 

of refuge management activities which are 

not economic in nature, all other uses are 

subservient to the NWRS’ primary wildlife 

management responsibility and they must 

be determined compatible before being 

authorized. 

The Refuge Improvement Act provides 

clear standards for management, use, 

planning, and growth of the NWRS. Its 

passage followed the promulgation of 

Executive Order 12996 (April 1996), 

“Management of Public Uses on National 

Wildlife Refuges”, reflecting the importance 

of conserving natural resources for the 

benefit of present and future generations 

of people. The Refuge Improvement 

Act recognizes that wildlife-dependent 

recreational uses including hunting, fishing, 

wildlife observation and photography, and 

environmental education and interpretation, 

when determined to be compatible with 

the mission of the System and purposes of 

the Refuge, are legitimate and appropriate 

public uses of the Refuge System. Section 

5 (C) and (D) of the Refuge Improvement 

Act states “compatible wildlife-dependent 

recreational uses are the priority general 

public uses of the Refuge System and shall 

receive priority consideration in planning 

and management; and when the Secretary 

determines that a proposed wildlifedependent recreational use is a compatible 

use within a refuge, that activity should be 

facilitated, subject to such restrictions or 

regulations as may be necessary, reasonable, 

and appropriate.”

The Refuge Improvement Act also directs 

the Service to maintain adequate water 

quantity and quality to fulfill the NWRS 

mission and refuge purposes, and to acquire, 

under state law, water rights that are needed 

for refuge purposes.

Compatibility Policy

Lands within the NWRS are different 

from other multiple use public lands in 

that they are closed to all visitor uses 

unless specifically and legally opened. 

The Improvement Act states that “. . . the 
 Stone Lakes NWR Comprehensive Conservation Plan

Secretary shall not initiate or permit a 

new use of a Refuge or expand, renew, or 

extend an existing use of a Refuge, unless 

the Secretary has determined that the 

use is a compatible use and that the use is 

not inconsistent with public safety.” The 

Improvement Act also states that “. . . 

compatible wildlife-dependent recreational 

uses (hunting, fishing, wildlife observation 

and photography, or environmental 

education and interpretation) are the 

priority general public uses of the System 

and shall receive priority consideration in 

Refuge planning and management.”

In accordance with the Improvement Act, 

the Service has adopted a Compatibility 

Policy (603 FW 2) that includes guidelines 

for determining if a use proposed on a 

national wildlife refuge is compatible with 

the purposes for which the refuge was 

established. A compatible use is defined 

in the policy as a proposed or existing 

wildlife-dependent recreational use or any 

other use of a national wildlife refuge that, 

based on sound professional judgment, will 

not materially interfere with or detract 

from the fulfillment of the NWRS mission 

or the purposes for which the Refuge 

was established and contributes to the 

maintenance of biological integrity, diversity, 

and environmental health. The Policy also 

includes procedures for documentation and 

periodic review of existing refuge uses.

When a determination is made as to whether 

a proposed use is compatible or not, this 

determination is provided in writing and is 

referred to as a compatibility determination. 

An opportunity for public review and 

comment is required for all compatibility 

determinations. For compatibility 

determinations prepared concurrently with 

a CCP or step-down management plan, the 

opportunity for public review and comment 

is provided during the public review period 

for the draft plan and associated NEPA 

document. The Refuge has completed 

compatibility determinations for fishing, 

wildlife observation and photography, 

environmental education and interpretation, 

high speed boating, recreational boating, 

research, grazing, plant collecting, and 

mosquito monitoring and control. These 

compatibility determinations will be 

finalized with the CCP. The compatibility 

determinations prepared in association with 

this draft CCP/EA are provided in Appendix 

A. 

Biological Integrity, Diversity, and 

Environmental Health Policy

Section 4(a)(4)(B) of the Refuge 

Improvement Act states, “In administering 

the System, the Secretary shall...ensure 

that the biological integrity, diversity, 

and environmental health of the System 

are maintained for the benefit of present 

and future generations of Americans...” 

This legislative mandate represents 

an additional directive to be followed 

while achieving refuge purposes and the 

NWRS mission. The Act requires the 

consideration and protection of a broad 

spectrum of fish, wildlife, plant, and habitat 

resources found on a refuge. Service policy 

guiding implementation of this statutory 

requirement provides a refuge manager 

with an evaluation process to analyze 

his/her refuge and recommend the best 

management direction to prevent further 

degradation of environmental conditions; 

and, where appropriate, and in concert with 

refuge purposes and NWRS mission, to 

restore lost or severely degraded resource 

components. Within the Biological Integrity, 

Diversity, and Environmental Health 

Policy (601 FW 3[3.7B]), the relationships 

among biological integrity, diversity, and 

environmental health; NWRS mission; 

and refuge purposes are explained as 

follows, “...each refuge will be managed 

to fulfill refuge purpose(s) as well as to 

help fulfill the System mission, and we 

will accomplish these purpose(s) and our 

mission by ensuring that the biological 

integrity, diversity, and environmental health 

of each refuge are maintained and where 

appropriate, restored.”

When evaluating the appropriate 

management direction for refuges, Refuge 
Stone Lakes NWR Comprehensive Conservation Plan 

Managers will use sound professional 

judgment to determine their refuge’s 

contribution to biological integrity, diversity, 

and environmental health at multiple 

landscape scales. Sound professional 

judgment incorporates field experience, an 

understanding of the refuge’s role within 

an ecosystem, and the knowledge of refuge 

resources, applicable laws and best available 

science, including consultation with resource 

experts both inside and outside of the 

Service.

The priority visitor uses of the NWRS are 

not in conflict with this policy when they 

have been determined to be compatible. 

The directives of this policy do not envision 

or necessitate the exclusion of visitors or 

the elimination of visitor use structures 

from refuges; however, maintenance and/or 

restoration of biological integrity, diversity, 

and environmental health may require 

spatial or temporal zoning of visitor use 

programs and associated infrastructures. 

General success in maintaining or 

restoring biological integrity, diversity, and 

environmental health will produce higher 

quality opportunities for providing wildlifedependent recreational uses.

Draft Wilderness Stewardship Policy 

Pursuant to the Wilderness Act of 1964

This policy updates guidance on 

administrative and public activities on 

wilderness and proposed wilderness within 

the NWRS. The purpose of the policy is to 

prescribe how the Service:

“...preserves the character and qualities of 

designated wilderness while managing for 

the refuge establishing purpose(s), maintains 

outstanding opportunities for solitude and 

primitive and unconfined type of recreation, 

and conducts minimum requirements 

analyses before taking any action that may 

impact wilderness character.”

The policy emphasizes recreational uses that 

are compatible and wilderness-dependent. 

The policy clarifies conditions upon which 

generally prohibited uses (motor vehicles, 

motorized equipment, mechanical transport, 

structures, and installations) may be 

necessary for wilderness protection. It 

confirms that: 

“...we will generally not modify habitat, 

species population levels, or natural 

ecological processes in refuge wilderness 

unless doing so maintains or restores 

ecological integrity that has been degraded 

by human influence or is necessary to 

protect or recover threatened or endangered 

species.”

National Environmental Policy Act of 

1969

This Draft CCP and associated National 

Environmental Policy Act (NEPA) document 

has been prepared consistent with the 

requirements of NEPA, the Council on 

Environmental Quality (CEQ) NEPA 

regulations (40 CFR Secs. 1500 et seq.), 

and the Department of Interior’s NEPA 

procedures (Department Manual, Part 516). 

Stone Lakes National Wildlife Refuge 

Location 

The Refuge is located in southern 

Sacramento County, west of the city of Elk 

Grove. It lies within the Morrison Creek, 

Cosumnes River and Mokelumne River 

watersheds as well as the Sacramento-San 

Joaquin Delta (Delta) (Figure 1. Ecoregion 

and Watershed Map). The approved Refuge 

boundary is roughly defined by Morrison 

Creek to the north, Franklin Boulevard and 

Interstate-5 to the east, the former Southern 

Pacific Railroad to the west and Lost Slough 

to the south. 

Refuge Setting 

Before European settlement, the BeachStone Lakes Basin was a magnet for wildlife, 

such as elk (Cervus elaphus), pronghorn 

(Antilocapra americana) and grizzly bear 

(Ursus arctos horribilis). During winter 

storms, the flooded basin could stretch from 

lower Morrison Creek to the Mokelumne 

River, expanding lakes and seasonal 

wetlands that supported tens of thousands 

of migratory birds. The land destined to 

become a national wildlife refuge teemed 

with wildlife.

The Plains Miwok relied on the land, its 

plants and its abundant wildlife for survival. 

These American Indians camped, hunted 

and fished along the shores of the area’s 
 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes

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Figure 1. Watershed and

Ecosystem Setting

Stone Lakes

Sacramento River Watershed

Central Valley-San Francisco

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National Wildlife Refuge

Kilometers 0 100

I

0 Miles 100
Stone Lakes NWR Comprehensive Conservation Plan 

lakes. Historic Beach Lake once covered 

nearly 1,000 acres and North and South 

Stone Lakes were also extensive. Located in 

the heart of the Refuge, the lakes received 

their names in the mid 1800s from a former 

landowner, a Sacramento merchant named 

Rockwell Stone. The Stone family held 

about 1,000 acres until 1891. 

Changes began in the mid 1800s. Levees 

were constructed along the Sacramento 

River and around Delta islands so the land 

could be farmed. The Southern Pacific 

Railroad was built, bisecting the basin, 

allowing nearly complete drainage of its 

lakes. Finally, Interstate-5 was constructed, 

ushering in tremendous pressure for urban 

development. 

As Sacramento grew in the mid 1960s, the 

U.S. Army Corps of Engineers (USACE) 

suggested building channels in the 

area to hold floodwaters. Conservation 

organizations also became interested in the 

basin in late 1960s, hoping to avoid a major 

flood control project and keep the area 

natural. During the same period, a local 

landowner proposed build a new town for 

50,000 people around North Stone Lake. 

In response to these pressures and in 

recognition of the importance of the 

Stone Lakes Basin floodplain, the State 

of California and County of Sacramento 

purchased about 2,600 acres in the 1970s, 

turning the land over to their respective 

park departments to manage. 

By the late 1980s the idea of further 

protecting the Stone Lakes Basin by 

establishing a national wildlife refuge took 

hold. Support for the Refuge derived partly 

from the fact that the unique lakes and 

waterways of the basin lie entirely within the 

100-year floodplain. The basin also occupies 

a strategic location for buffering the effects 

of urban encroachment into the Delta. 

Additionally, a national wildlife refuge could 

potentially provide a link with ongoing 

nearby land conservation efforts such as the 

Cosumnes River Preserve. 

Several local legislators supported 

protecting the land from development and 

were in a position to help move the process 

forward. 

History of Refuge Establishment and 

Acquisition

In July 1992, the Service completed a 

complex two year public planning process 

resulting in 

finalization of an 

environmental 

impact statement 

(EIS). The EIS 

(USFWS 1992) 

defined the present 

18,000 acre 

approved Refuge 

boundary. 

During circulation 

of the draft EIS, , 

the Service received 

written and verbal 

input from over 

6,000 citizens about 

potential effects a 

refuge could have on 

the landscape and 

the EIS’ adequacy 

in addressing these issues. Despite litigation 

under NEPA over the adequacy of the EIS , 

the Service successfully defended its Record 

of Decision and with a broad base of local 

support, established the Refuge in 1992. 

With acquisition of the first property in 1994, 

the Refuge was officially established as the 

505th unit in the National Wildlife Refuge 

System. It joined the ranks of other local 

land conservation and management projects, 

including the Cosumnes River Preserve to 

the southeast and the Vic Fazio Yolo Bypass 

Wildlife Area to the west, which have similar 

goals of protecting and enhancing vital 

Central Valley fish and wildlife habitats. 

Land Protection

The approved boundary for the Refuge 

is the area within which the Service is 

authorized to work with willing landowners 

to acquire and/or manage land (Figure 

2. Land Status). The Refuge consists 

of an approximately 9,000 acre core area 

With a broad base 

of local support 

the Refuge was 

established in 1992, 

protecting habitat 

for native species 

like this redshouldered hawk.

Photo by Tom Harvey, 

USFWS
 Stone Lakes NWR Comprehensive Conservation Plan

(Figure 3. Core and Cooperative Wildlife 

Management Areas), encompassing Upper 

and Lower Beach Lakes and North and 

South Stone Lakes and an approximately 

9,000 acre Cooperative Wildlife Management 

Area (CWMA), encompassing lands to the 

east and south of the core area. Within the 

approved Refuge Boundary, the Service 

may pursue a number of approaches to 

conserve and manage lands, depending 

on the preferences of willing landowners. 

These may include: technical assistance, 

cooperative agreements, memoranda 

of understanding and acquisition of 

conservation or agricultural easements 

and fee title interest. In the EIS (USFWS 

1992), the Service agreed to use fee title 

acquisition within the CWMA only on 

a case by case basis and after seeking 

approval by the Sacramento County Board 

of Supervisors. The preferred approaches 

to conserve lands within the CWMA are: 

cooperative agreements, memoranda of 

understanding, and purchase of conservation 

or agricultural easements. According to the 

August 1992 Land Protection Plan for The 

Refuge, a primary objective of the CWMA is 

to maintain lands in private ownership and 

continue agricultural production.

To date, the Service manages approximately 

6,000 acres within the approved project 

boundary including: 2,617.9 acres under 

cooperative agreements; 1,738.8 acres in 

fee title ownership; and 1,519.9 acres under 

agricultural easement. Approximately 

11,622 acres of non-refuge lands lie within 

the approved refuge boundary.

The Service is also exploring cooperative 

management of an additional 2,210 acres 

within the approved boundary that 

are owned by two other agencies: (1) 

Sacramento Regional Sanitation District 

(1,800 acres); and (2) California Department 

of Water Resources (410 acres). 

Land Conservation Methods

Working with willing landowners and local 

and state agencies, the Service may use 

various means to conserve or manage fish 

and wildlife and their habitats within the 

approved Refuge boundary. These may 

include: fee title acquisition, conservation 

easements, memoranda of understanding 

and cooperative agreements, financial 

incentives and technical assistance and 

education and outreach. It is the established 

policy of the Service to seek the minimum 

degree of interest in property needed 

to accomplish refuge land conservation 

objectives.

In fee title acquisitions, the Service acquires 

full ownership of property through fee 

simple purchase, donation, exchange, or 

transfer from another Federal agency. 

Land acquired in fee title by the Service is 

removed from county tax roles. To partially 

offset this loss, the Service provides annual 

payments to counties as authorized by the 

Refuge Revenue Sharing Act (Public Law 

95-469). The Service is required under the 

U.S. Constitution to pay fair market value 

for property and purchases are dependent 

on the availability of funds.

In acquiring a conservation easement, the 

Service purchases the minimum rights 

needed to conserve fish and wildlife habitat, 

while allowing the existing landowner to 

retain title to the land. Easements may 

include wetland or waterfowl habitat 

easements, upland easements, agricultural 

practices easements and non-development 

easements. The easement interest acquired 

by the Service becomes part of the Refuge 

and is subject to applicable laws and 

regulations pertaining to refuges. The 

easement is a permanent interest in the 

property that runs with the land and the 

landowner remains responsible for all 

property taxes About 5,000 acres within the 

approved Refuge boundary and CWMA are 

currently publicly owned and managed for 

conservation purposes by five local and State 

agencies. A majority of these lands are or 

will be jointly managed with the Service 

through memoranda of understanding and 

cooperative agreements.

The Service may also assist in securing 

financial incentives for landowners who 

are not willing to sell an interest in their 

property but wish to explore conservation 

or enhancement of fish and wildlife habitats 
Stone Lakes NWR Comprehensive Conservation Plan

Sacramento River

160

5

North

Stone

Lake

Twin Cities Rd

Snodgrass Slo u gh

Lambert Rd

Elk Grove Blvd

Hood Franklin Rd

Franklin Blvd.

South

Stone

Lake

Southern Pacific Railroad (abandoned)

Figure 2. Land Status

National Wildlife Refuge

Refuge Headquarters

Cooperative Agreement

Conservation Easement

County or State Land

Private Ownership

Owned in Fee Title

Approved Refuge Boundary

Stone Lakes

0 0.5 1 2

Miles

0 0.5 1 2

Kilometers
10 Stone Lakes NWR Comprehensive Conservation Plan

1 0.5 0 1Miles

Cooperative Wildlife Management Area

Stone Lakes NWR Core Area

Owned in Fee Title

Conservation Easements

Cooperative Agreements

Other Lands

FIgure 3. Stone Lakes NWR Project Area

National Wildlife Refuge

Stone Lakes

1 0.5 0 1Kilometers
Stone Lakes NWR Comprehensive Conservation Plan 11

on their property. For example, through 

the Partners for Fish and Wildlife program, 

landowners may apply for financial 

assistance from the Service to protect, 

enhance, or restore wetland, riparian, 

or native grassland habitats on their 

property. In addition, the Service could 

assist a landowner to secure funds from 

Farm Bill programs available from the 

U.S. Department of Agriculture/Natural 

Resources Conservation Service (NRCS). 

Potential NRCS programs that could 

benefit landowners and further Refuge 

land conservation objectives include the: 

Conservation of Private Grazing Land 

Program, Environmental Quality Incentives 

Program, Farmland Protection Program, 

Wetlands Reserve Program and Wildlife 

Habitat Incentives Program. Finally, 

Service staff is available to provide technical 

assistance and education and outreach 

information to willing landowners who are 

interested in conserving fish and wildlife 

habitats on their lands. 

The Refuge has financed most of its land 

acquisition and restoration efforts with 

grants from a wide range of state and 

federal agencies and private organizations. 

These sources have played a vital role in 

advancing the Refuge’s land conservation 

and management programs. Grants have 

been provided by: City of Sacramento, 

County of Sacramento, California 

Wildlife Conservation Board, California 

Environmental Enhancement Mitigation 

Fund, California Environmental License 

Plate Fund, Cigarette and Tobacco Product 

Surtax, Department of Transportation-TEA 

21 Fund, CALFED Bay Delta Program, 

North American Wetlands Conservation Act, 

Land and Water Conservation Fund, Central 

Valley Project Improvement Act, National 

Fish and Wildlife Foundation, David and 

Lucille Packard Foundation, The Trust for 

Public Land and other private donations. 

Partnerships

Partnerships have been a cornerstone of 

Refuge development and management. 

A consortium of public and private 

organizations strongly supported the 

designation of Stone Lakes as a national 

wildlife refuge and has since been joined by 

many others as the Refuge has expanded. 

The Refuge’s urban location and the local 

and state agencies that own land within the 

Refuge boundary have provided numerous 

opportunities for partnerships from the 

Refuge’s inception.

 

The Refuge staff routinely discusses and 

coordinates restoration activities, jointly 

applies for grants and discusses other 

management issues with the Sacramento 

County Department of Regional Parks, 

Recreation and Open Space (North Stone 

Lake Unit ), the Sacramento Regional 

County Sanitation District (Bufferlands) 

and the California Departments of 

Transportation (Caltrans) (Beach Lake 

Mitigation Bank), California Department of 

Parks and Recreation (DPR) (North Stone 

Lake Unit) and California Department of 

Water Resources (DWR) . The Service 

has finalized a cooperative agreement 

with Sacramento County Department of 

Regional Parks, Recreation and Open Space 

over management of the North Stone Lake 

unit and partners closely with Sacramento 

Regional County Sanitation District on the 

annual event, Walk on the Wildside, and the 

water hyacinth control program. 

Controlling water hyacinth a nonnative, 

invasive aquatic plant, has been a prime 

motivation for formation of an important 

partnership, the Stone Lakes Water 

Hyacinth Working Group, in which the 

Refuge plays a central role. This group 

includes more than a dozen local and 

state agencies, organizations, and private 

individuals who own or manage land 

in the Stone Lakes Basin, affected by 

this noxious weed. Recent partners in 

the group have included: the Refuge, 

California Department of Boating and 

Waterways (DBW), Sacramento Regional 

County Sanitation District (SRCSD), 

Sacramento County Supervisor Don Notolli, 

Sacramento County Department of Water 

Resources, Sacramento County Agricultural 

Commission, Sacramento-Yolo Mosquito and 
12 Stone Lakes NWR Comprehensive Conservation Plan

Vector Control District (SYMVCD), Florin 

Resource Conservation District, Caltrans, 

Vino Farms, the Whitney Family, LaRue 

Schock and the San Francisco Estuary 

Institute. The working group cooperates 

on eradication, has applied for and received 

grants and has produced educational 

materials to reduce the spread of water 

hyacinth in local waterways.

The Refuge also coordinates with California 

Departments of Fish and Game (DFG) and 

DBW , Resource Conservation District 

#813 and Sacramento County Department 

of Environmental Review on issues of 

mutual management concern. Much 

of the restoration that has occurred on 

Refuge managed land occurred through 

partnerships with a variety of private 

organization, including Ducks Unlimited, 

California Waterfowl Association, Wildlands, 

Inc., Stone Lakes National Wildlife Refuge 

Association, American Lands Conservancy, 

Sacramento Tree Foundation, Safari Club, 

and Trust for Public Land.

The Service entered into a Memorandum 

of Understanding (MOU) with SYMVCD 

in 1993 to address concerns regarding 

potential effects the Refuge may have on 

mosquito populations. According to the 

MOU, the Service agreed to consult with 

SYMVCD on the design and management 

of Refuge wetlands and provide access 

to SYMVCD to monitor the mosquito 

population on the Refuge. The Service also 

agreed to submit Pesticide Use Proposals 

for pesticides SYMVCD may wish to use on 

the Refuge, if thresholds for larval or adult 

control are exceeded. SYMVCD and the 

Service rely on a full range of integrated 

pest management techniques to manage 

mosquito populations, including water and 

vegetation management, biological control 

(e.g., planting of mosquito fish [Gambusia 

affinis]) and if necessary, chemical control 

of larval or adult mosquitoes. As a result, 

mosquito larval control activities since 1994 

have been largely limited to localized (less 

than five acres) applications of larvicides and 

until 2005, and only three applications of an 

adulticide. 

In 2005, West Nile Virus (WNV) became 

established in Sacramento and Yolo counties, 

triggering aggressive and widespread 

mosquito control efforts. In August of 2005 

the number of human WNV cases and rate 

of infected adult mosquitoes were so high 

that SYMVCD conducted aerial applications 

of pyrethrin over a major portion of 

Sacramento County (Sacramento County 

2006). During 2005, the Refuge received 

ultra-low volume (ULV) ground treatments 

of pyrethrin on 18 occasions from September 

28 through October 12. As of July 2006, 

the Refuge has been adulticided six times 

between June 27 and July 21.

The Service also cooperates with SYMVCD 

in the monitoring of landbird populations 

on the Refuge, primarily to evaluate the 

role of wild bird populations as reservoirs of 

mosquito-borne diseases, such as western 

equine encephalitis, St. Louis encephalitis, 

and West Nile Virus. The landbird 

monitoring program began in 1995 and 

involves mist netting and banding of a wide 

variety of birds. A small blood sample (0.10 

cc) is taken from some species for disease 

analysis. In addition to contributing to the 

goals of mosquito management, the program 

has provided valuable information regarding 

bird use on the Refuge, timing of migration, 

reproductive ecology and reproductive 

success.

In addition to those already mentioned, 

Controlling and 

eliminating 

invasive water 

hyacinth, shown 

here being removed 

from Lambert 

Ditch by volunteers, 

was the prime 

motivation for 

another important 

partnership: the 

Stone Lakes Water 

Hyacinth Working 

Group.

Photo by USFWS
Stone Lakes NWR Comprehensive Conservation Plan 13

several programs and nongovernmental 

organizations (NGOs) provide vital support 

for Refuge land conservation, restoration 

and visitor services programs, including 

the CALFED Bay Delta Authority 

Ecological Restoration Program, Central 

Valley Project Improvement Act, North 

American Wetlands Conservation Act, 

Audubon California, California Native Plant 

Society, California Waterfowl Association, 

The Nature Conservancy and Sacramento 

Open Space. These groups routinely 

assist with grant writing and fundraising, 

coordinate research or census efforts, help 

with planning programs and activities and 

provide coverage of Refuge activities in their 

publications or events. 

Refuge Purposes 

Lands within the Refuge System are 

acquired and managed under a variety of 

legislative acts and administrative orders 

and authorities. The official purpose or 

purposes for a refuge are specified in 

or derived from the law, proclamation, 

executive order, agreement, public land 

order, funding source, donation document, or 

administrative memorandum establishing, 

authorizing, or expanding a refuge, refuge 

unit, or refuge subunit. The purpose of 

a refuge is defined when it is established 

or when new land is added to an existing 

refuge. When an addition to a refuge is 

acquired under an authority different from 

the authority used to establish the original 

refuge, the addition takes on the purposes 

of the original refuge, but the original 

refuge does not take on the purposes of the 

addition. Refuge managers must consider 

all of the purposes. However, purposes that 

deal with the conservation, management, 

and restoration of fish, wildlife and plants 

and their habitats take precedent over 

other purposes in the management and 

administration of a refuge. 

The Refuge System Improvement Act 

directs the Service to manage each refuge to 

fulfill the mission of the Refuge System, as 

well as the specific purposes for which that 

refuge was established. Refuge purposes 

are the driving force in developing refuge 

vision statements, goals, objectives and 

strategies in the CCP. Refuge purposes are 

also critical to determining the compatibility 

of all existing and proposed refuge uses.

Stone Lakes National Wildlife Refuge 

was established under the authority of the 

Emergency Wetlands Resources Act of 

1986, the Fish and Wildlife Act of 1956, The 

Migratory Bird Conservation Act and The 

Endangered Species Act of 1973. 

According to these authorities, the Refuge 

purposes are:

 “... for the conservation of the wetlands of 

the Nation in order to maintain the public 

benefits they provide and to help fulfill 

international obligations contained in various 

migratory bird treaties and conventions ...” 

16 U.S.C. §§ 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, 

management, conservation, and protection 

of fish and wildlife resources ...” 16 U.S.C. 

§§ 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of 

servitude ...” 16 U.S.C. §§ 742f(b)(1) (Fish 

and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or 

for any other management purpose, for 

migratory birds.” 16 U.S.C. §§ 715d 

(Migratory Bird Conservation Act)

“... to conserve (A) fish or wildlife which are 

listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. §§ 

1534 (Endangered Species Act of 1973) 

Related Projects and Studies in the 

Area

U.S. Fish and Wildlife Service 

Final Environmental Impact Statement 
14 Stone Lakes NWR Comprehensive Conservation Plan

Stone Lakes National Wildlife Refuge 

(EIS). In 1972, Jones and Stokes Associates 

prepared an EIS for the Refuge. The 

purpose of the EIS was to evaluate the 

effects of various Service alternatives to 

acquire and protect lands in southwestern 

Sacramento County to establish the 

Refuge. The EIS includes interim Refuge 

management goals and proposed habitat 

restoration areas.

The interim Refuge management goals are 

as follows:

• Preserve, enhance, and restore a diverse 

assemblage of native Central Valley plant 

communities and their associated fish, 

wildlife and plants;

• Preserve, enhance, and restore habitat to 

maintain and assist in the recovery of rare, 

threatened, and endangered plants and 

animals;

• Preserve, enhance, and restore wetlands 

and adjacent agricultural lands to provide 

foraging and sanctuary habitat needed to 

achieve the distribution and population 

levels of migratory waterfowl and other 

water birds consistent with the goals 

and objectives of the North American 

Waterfowl Management Plan and Central 

Valley Habitat Joint Venture;

• Create linkages between refuge habitats 

and habitats on adjacent lands to reverse 

past impacts of habitat fragmentation on 

wildlife and plants;

• Coordinate refuge land acquisition and 

management activities with other agencies 

and organizations to maximize the 

effectiveness of refuge contributions to 

regional habitat needs;

• Provide for environmental education, 

interpretation and fish and wildlife 

oriented recreation in an urban setting 

accessible to large populations; and

• Manage riverine wetlands and adjacent 

floodplain lands in a manner consistent 

with local, State and Federal flood 

management; sediment and erosion 

control, and water quality objectives.

Draft North Stone Lake Management 

and Restoration Plan. The 2,791 acre 

North Stone Lake Unit consists of two 

adjacent parcels owned by the DPR 

(1,224 acres) and Sacramento County 

(1,567 acres). The goal of the Service is to 

cooperatively manage both these properties 

with the County and the State, as a unit of 

the Refuge. The Service currently has a 

cooperative agreement with Sacramento 

County for management of their property 

and is drafting an agreement with DPR 

that addresses the State-owned land. Since 

Sacramento County has managed both 

parcels collectively as the North Stone Lake 

Wildlife Refuge, they drafted a management 

and restoration plan in 1992. The plan 

has now been revised and updated by the 

Service. Some wetland restoration elements 

in the 1992 plan that were not considered to 

have neutral effects on floodplain storage 

were removed or modified in the revision 

but the plan has not been adopted by 

Sacramento County. . Under the revised 

draft plan, the North Stone Lake Unit 

would be managed for a diversity of native 

animal and plant species by enhancing 

and restoring a diversity of wetland and 

grassland habitats. Once completed, many 

of the restoration projects will require little 

management. Other restored habitats, 

such as seasonal marshes and grasslands, 

will require intensive management and 

manipulation.

Other Agencies and Projects 

Sacramento Regional Wastewater 

Treatment Plant and Bufferlands. The 

Sacramento Regional County Sanitation 

District (SRCSD) constructed the 

Sacramento Regional Wastewater Treatment 

Plant (SRWTP) to treat wastewater for the 

urbanized area of Sacramento. In addition 

to constructing the plant, SRCSD purchased 

2,650 acres surrounding the treatment plant 

to serve as a buffer between the plant and 

surrounding planned and existing residential 

communities. This land is known as the 

Bufferlands. Approximately 1,800 acres 

of the Bufferlands lie within the approved 

Refuge boundary The Service and SRCSD 

have drafted a cooperative management 

agreement for the Bufferlands to be 

managed a unit of the Refuge. SRCSD 

restores native habitats such as wetlands, 

riparian forest, and native grasslands and 

actively manages the Bufferlands as wildlife 
Stone Lakes NWR Comprehensive Conservation Plan 15

habitat. They also provide opportunities for; 

environmental education, interpretation, 

wildlife observation and fishing; oversee a 

volunteer program and partner with the 

Service and others on the annual Refuge 

event, Walk on the Wildside.

Vic Fazio Yolo Basin Wildlife Area. The 

Vic Fazio Yolo Wildlife Area is managed 

by the California Department of Fish and 

Game and located along Interstate-80 where 

16,000 acres in the Yolo Bypass floodway 

have been restored to wetlands or support 

agricultural lands managed for the benefit 

of fish and wildlife. . The Wildlife Area lies 

approximately 15 road miles northwest of 

the Refuge and was created through the 

cooperative efforts of an array of private, 

State and Federal partners. It covers 

approximately six square miles and provides 

visitor opportunities such as bird watching, 

outdoor educational programs and waterfowl 

hunting.

Cosumnes River Preserve. The Cosumnes 

River Preserve is located adjacent to 

and southeast of the Refuge’s approved 

boundary and just upstream from the 

confluence of the Cosumnes and Mokelumne 

rivers. The Preserve was established 

through the cooperative efforts of a private/

public partnership that includes The Nature 

Conservancy, Ducks Unlimited, U.S. 

Bureau of Land Management, Sacramento 

County and California Department of Water 

Resources. The project strives to conserve 

and enhance nearly 46,000 acres of riparian 

forest, wetlands and grasslands along the 

Cosumnes River, which is the only remaining 

un-dammed tributary of the Sacramento 

River. 

The Cosumnes River floodplain provides 

habitat for tens of thousands of migratory 

waterfowl, songbirds and birds of prey; 

a large portion of the Central Valley’s 

population of greater sandhill cranes (Grus 

canadensis tabida); and rare reptiles and 

mammals, such as the endangered giant 

garter snake (Thamnophis gigas). Chinook 

salmon (Oncorhynchus tshawytscha) and 

Pacific lamprey (Lampetra tridentate) spawn 

and native Delta fish breed and rear their 

young in the shallow waters of the wetlands. 

The Central Valley Joint Venture. The 

Central Valley Joint Venture (CVJV) is 

a partnership of private conservation 

organizations and State and Federal 

agencies whose goal is to protect, maintain 

and restore habitat to increase Central 

Valley waterfowl populations to levels 

comparable to the 1970s and consistent with 

other objectives of the North American 

Waterfowl Management Plan. The Central 

Valley of California is the most important 

waterfowl wintering area in the Pacific 

Flyway, supporting 60 percent of the 

flyway’s duck and goose population. It is 

especially important that 65 percent of all 

pintails (Anas acuta) in the United States 

use the Central Valley. 

CALFED Bay-Delta Authority 

(CALFED). CALFED, a consortium 

of stakeholders and State and Federal 

agencies, is attempting to develop a plan 

to address water supply and flood control 

concerns, as well as restoration of fish and 

wildlife populations of the Sacramento-San 

Joaquin Delta (Delta). Under CALFED’s 

ecological restoration program funding was 

made available to purchase the Sun River 

portion of the South Stone Lake Unit. 

Central Valley Project Improvement Act 

(CVPIA).

The CVPIA was adopted to incorporate 

The Cosumnes 

River floodplain 

provides habitat for 

tens of thousands 

of migratory 

waterfowl, 

songbirds, and 

birds of prey; a 

large portion of the 

Central Valley’s 

population of 

greater sandhill 

cranes; and 

uncommon reptiles 

and mammals, such 

as these river otters. 

Photo by USFWS
16 Stone Lakes NWR Comprehensive Conservation Plan

conservation and enhancement of fish and 

wildlife populations into operation of the 

Central Valley Project by the U.S. Bureau of 

Reclamation. It provides for the allocation 

of water supplies for the recovery of native 

fishes and for State and Federal wildlife 

management areas. Funding available 

through the program assisted the Refuge 

with acquisition of the Headquarters Unit.
Stone Lakes NWR Comprehensive Conservation Plan 17

2 The Planning Process

The Planning Process 

The Refuge Planning Chapter of the Fish 

and Wildlife Service Manual (Part 602 FW 

2.1, November 1996) and evolving policy 

related to the Refuge System Improvement 

Act of 1997 help to guide the process 

followed for developing this Comprehensive 

Conservation Plan (CCP). Key steps 

include: 

• Gathering information;

• Initiating public involvement;

• Analyzing resource relationships;

• Identifying issues and developing vision 

and goals; 

• Developing alternatives and assessing 

environmental effects; 

• Identifying a preferred alternative; 

• Publishing the draft CCP and NEPA 

document; 

• Documenting public comments on the 

draft CCP; 

• Revising the draft CCP and preparing the 

final CCP; 

• Securing approval of the California/

Nevada Operations; and 

• Implementing the CCP. 

The CCP may be amended at any time, as 

necessary, under an adaptive management 

strategy. Public involvement and NEPA 

review will be required if major revisions are 

needed.

The Stone Lakes CCP Process

In a Federal Register Notice, dated August 

26, 2002, the Service announced that it was 

preparing a CCP for the Refuge. The first 

Refuge planning update, distributed in July 

2002, provided the public with background 

about the Refuge and the National Wildlife 

Refuge System and explained how CCP 

development fits into the overall picture of 

refuge management.

The second planning update, released in 

September 2002, announced a series of 

the public meetings and explained how the 

public could become involved in the planning 

process. The purpose of the meetings was 

to solicit public involvement in the CCP 

process and help Service staff identify issues 

and gather information to help develop the 

CCP.

This draft CCP and Environmental 

Assessment (EA) (Appendix B) are being 

distributed to Refuge cooperators, nearby 

landowners, State and Federal government 

agencies, local jurisdictions, private 

organizations, community groups and 

private citizens. The public has 30 days from 

the draft’s release to provide comments. A 

final planning update will be issued at the 

same time as the final CCP. The draft CCP 

and EA can also be viewed at the following 

internet sites: http://stonelakes.fws.gov/

publicreview.htm and http://library.fws.gov/

ccps.htm.

The CCP will assist Refuge staff with 

preparation of annual work plans and 

updating the Refuge Operational Needs 

System (RONS) database. The RONS 

database describes the unfunded budget 

needs for each refuge and is the basis upon 

which funding increases are allocated for 

operational needs. The plan may also be 

reviewed during routine inspections or 

programmatic evaluations. Results of the 

reviews may indicate a need to modify the 

plan. Periodic review of the objectives and 

strategies is an integral part of the plan, 

and management activities may be modified 

if the desired results are not achieved. 

Depending on the degree that changes may 

be required, the appropriate level of public 

involvement and NEPA documentation will 

be determined by the Refuge Manager. The 

CCP will be formally revised every 15 years.
18 Stone Lakes NWR Comprehensive Conservation Plan

Issues Identified by the Public 

During the CCP public scoping process, 

issues, concerns, and opportunities were 

identified through public meetings, 

discussions with planning team members 

and other key contacts. The public had 

an opportunity to attend four scoping 

meetings, in Elk Grove, Davis, Walnut 

Grove and Sacramento, where their 

comments were recorded. More than 135 

people attended these meetings. Over 250 

people also provided written comments 

by mail and e-mail and through personal 

conversations with the Refuge and planning 

staffs. During the planning process, the 

Service has received numerous comments 

and suggestions regarding the potential 

for public hunting on the Refuge. Due to 

opportunities related to recent conveyance 

of the Sun River property to the Refuge and 

commitments by the Service to maintain 

hunting opportunities in the South Stone 

Lake area, the Refuge opted to establish 

a public waterfowl hunting program 

during 2005-2006 through a separate 

planning process, independently of this 

CCP. All comments, issues, concerns, and 

opportunities compiled by the Service are 

summarized in the following narrative which 

has been organized by several broad topics.

Management 

Several meeting attendees observed that 

the future of Refuge wildlife will rely on 

establishing sanctuary areas separate from 

visitor use areas, or establishing times 

within use areas when wildlife are not 

disturbed. They asked that visitor uses 

be compatible with Refuge conservation 

purposes and that management decisions be 

based on resource values. One group asked 

the Service to assess the negative impacts 

of waterfowl management on other native 

plants and animals and asked the Service 

to mitigate the impacts of recreational 

activities. The same group also requested 

that the Service assess the effects of 

predator management strategies to protect 

sensitive, threatened and endangered 

species. Some hope to see Refuge staff work 

with the city of Elk Grove and Cosumnes 

River Preserve to develop an open space 

greenbelt to contain development.

A number asked about the Refuge land 

acquisition priorities and plans for potential 

acquisitions, hoping to see site specific 

plans developed for each property that is 

purchased. Others felt the Refuge needs 

more conservation easements and other land 

protection strategies. Specific reference 

was made to the areas east of Interstate-5 

and North of Hood-Franklin Road and also 

South of Lambert Road as places to favor 

easements over fee title acquisition.

Some local landowners would like to see a 

balance between historic land uses, such 

as agriculture, and expanded recreation 

opportunities. They suggested that the 

Refuge establish a 500-foot buffer zone for 

agricultural spraying and other historic 

farming activities to avoid problems between 

existing arming activities and Refuge 

activities and between privately owned lands 

and Refuge restoration activities. 

There were several comments about the 

Refuge’s floodplain location, the need to 

maintain its floodplain capabilities and 

concern regarding how proposed activities 

and landscape modifications would impact 

flooding. Refuge plans should leave room 

for Sacramento County or the State to deal 

Public comments, 

on Comprehensive 

Conservation 

Planning for 

the Refuge, were 

received in writing, 

via e-mail, via 

postal mail and 

during four public 

meetings. 

Photo by USFWS
Stone Lakes NWR Comprehensive Conservation Plan 19

with the Morrison Creek flood problem. 

They should also recognize that surrounding 

agricultural lands are on higher ground, 

providing a natural escape for animals 

during flooding. Because one of the Refuge’s 

goals is to expand or enhance threatened 

and endangered species, some neighboring 

landowners feel they need an incidental take 

provision that would allow them to continue 

their farming operations should flooding and 

endangered species displacement occur.

Along the same lines, concern was expressed 

about mosquito-related problems and the 

existing MOU with the Sacramento-Yolo 

Mosquito and Vector Control District. If an 

emergency occurs and action is required, 

there is concern that the bureaucracy will 

cause unnecessary delays that could impact 

neighboring private lands. They would 

like to see some sort of pre-approved plan 

established for such emergencies.

Some people commented that the Refuge 

must be a good neighbor and responsible 

landowner and help pay overhead costs, just 

as other private landowners. This means 

that the Refuge should pay water usage 

fees to the North Delta Water Agency and 

reclamation districts and pay mosquito 

abatement costs and other fees. Some feel 

this has been a source of frustration for ten 

years and that private landowners cannot 

subsidize public ownership

A few people asked how the Refuge acquires 

water rights. One attendee suggested 

that the Refuge should use treated 

wastewater because a pipe conveying 

treated water already passes through the 

Refuge. People would like to see water 

quality and groundwater monitored/tested. 

They would also like assurance that Elk 

Grove and Sacramento meet clean water 

standards before their runoff reaches the 

Refuge. An additional concern regarding 

waterways relates to the spread of water 

hyacinth (Eichhornia crassipes). A request 

was made for the Refuge to continue its 

cooperative program to manage/control 

water hyacinth and other noxious weeds.

There was a general recognition that Refuge 

management is labor intensive and that it 

should be a high priority for the Refuge 

to have adequate staffing and funding. A 

suggestion was made to charge day use fees 

for all activities to help cover management, 

expansion, fish stocking, etc. 

The Delta Protection Commission 

acknowledged the Refuge’s outreach efforts 

to invite comments during the CCP process. 

The Commission’s comment reflected their 

mission of keeping as much land in private 

ownership as is possible within the primary 

zone of the Delta and working with the 

habitat values associated with agriculture. 

The Refuge Staff was also extended an 

invitation to brief the Commission about 

CCP progress. 

General Access

Many comments expressed concern about 

the current lack of, or very limited access to 

the Refuge. There were numerous requests 

that the Refuge allow many more types 

of recreational activities and that these 

expanded opportunities occur soon.

Many types of recreational uses were 

mentioned. Hunting received the greatest 

number of requests, from both individuals 

and hunting organizations. Horseback 

riders and a water ski group have accessed 

portions of the Refuge from private lands 

since prior to its establishment and they 

asked for continued access. Comments 

asked for many other types of uses, including 

fishing, photography, hiking, bird watching, 

small boat launching facilities, bicycle trails, 

dog trials, environmental education, wildlife 

observation areas and facilities, picnic and 

day use facilities and a visitor center. They 

also requested restrooms. They suggested 

that the Refuge may want to consider 

camping or rustic lodging facilities. 

Some said that the Refuge should obtain the 

needed funding to fully staff daily operations 

to allow improved open access. Several 

meeting attendees expressed the belief that 

since this is Federal land, it is their right to 

have opportunities for these activities. And 

several offered to support these activities by 

helping to build facilities, patrol the Refuge, 

or perform other needed work.
20 Stone Lakes NWR Comprehensive Conservation Plan

Several comments asked that recreational 

uses be balanced, specifically requesting 

that hunting be balanced with other uses. 

They asked that recreational opportunities 

be allowed in a way that protects wildlife. 

They suggested that some activities, such as 

hunting and wildlife viewing, be restricted to 

specific areas or times to avoid conflicts.

To support their requests, several made 

comparisons to Yolo Basin Wildlife Area, 

observing that it originally had less land 

under management but supported more 

types and amount of usage, and to the 

American River Parkway, which allows 

considerable recreational usage. They 

suggested thinking about obtaining 

funding from other sources for these types 

of programs. A few attendees hoped 

that the Refuge would remain rustic and 

unimproved, calling this “symbolic.”

Many asked questions about or commented 

on the waterways as part of the public 

trust. They wanted to know if the Refuge’s 

waterways were considered navigable and 

what the Refuge policy would be regarding 

their use. Historic use of waterways was 

cited several times, as well as the belief that 

use of waterways should not be restricted. 

Boating/Waterskiing

Several comments asked that the Refuge 

provide opportunities for sculling, canoeing, 

and non-motorized boating or boating with 

trolling motors only; they also requested a 

ban on jet skis.

Comments fell on both sides of whether 

to allow waterskiing. Some felt it was 

inappropriate. Several members of the local 

water ski club that has used Beach Lake 

for many years asked the Refuge to allow 

this historic use to continue, citing that it 

is a very seasonal, limited use and does not 

conflict with other uses or wildlife. They 

suggested creating a designated waterski 

area. Several waterskiers offered to help 

the Refuge by picking up trash or acting as 

docents of the waterways.

The California Canoe and Kayak School, 

a paddling school and retail center in 

Northern California, asked if there would 

be an opportunity to open a commercial 

operation with docent led activities.

Horseback Riding

Several horseback riders who had accessed 

the Refuge through the privately owned 

Beach Lake Stables said there has been 

historical, “prescriptive” use of the Refuge 

for horseback riding since 1970. They would 

like to continue to ride on the Refuge, saying 

that there are only ten to 15 regular riders 

who ride seasonally. 

Some horseback riders attending the 

meetings asked that the Refuge be opened 

to riding, with designated areas for riding 

and other uses. They commented that riding 

is low impact and can coexist with wildlife 

and the six priority visitor uses. They would 

like the opportunity to show it is compatible 

and requested restrictions on horseback 

riding if there is a conflict with hunting. 

Several riders spoke of their willingness to 

respect the sensitivity of the ecosystem and 

remain on trails. They offered to organize a 

volunteer horse patrol, similar to the Lake 

patrol and help maintain trails and report 

poachers, vandalism, fires, etc. 

Others expressed concern as to whether 

horseback riding and hunting would be 

compatible with each other. One comment 

expressed concern about the environmental 

effects of horseback riding, particularly 

erosion.

Fishing 

Several comments asked about the Refuge’s 

plans regarding fishing. Some said they used 

to fish at Stone Lakes prior to its designation 

as a national wildlife refuge and would like 

the opportunity again. They would like yearround fishing, especially bass fishing. 

Comments suggested that fishing and 

hunting should be separated to avoid 

conflicts. One comment was that if hunting 

and fishing are allowed, the hunt area 

should be closed to fishing on hunt days. 

Another comment suggested that the 

Refuge should stock fish to provide good 

family experiences. The Refuge offers a 
Stone Lakes NWR Comprehensive Conservation Plan 21

great opportunity for reintroduction of 

Sacramento perch.

Hunting 

There is strong support for a hunting 

program that includes waterfowl and upland 

birds, including pheasant, dove, and quail. 

Many people mentioned that hunting has 

occurred historically at Lodi Gun Club and 

other parts of the Refuge both to support 

their request and as rationale for allowing 

interim hunting on some of these existing 

Refuge properties. A few attendees asked to 

include big game hunting, such as deer (with 

a shotgun) and small game, such as rabbit.

They also pointed out that hunting exists 

on other refuges. They feel that if the top 

third of the Refuge is closed to hunting due 

to County regulations and the bottom third 

is closed due to agricultural use, then the 

middle area south of Hood-Franklin Road 

should be developed for hunting, not as 

wildlife sanctuaries. They asked whether 

hunting could be allowed on the State and 

County properties that the Refuge manages. 

Several specifically requested that the 

Refuge establish an interim compatibility 

determination to allow hunting now. A 

few felt that a hunting program should 

be developed when suitable property and 

adequate staffing are available.

In terms of access, some feel that 

nonconsumptive uses, such as wildlife 

viewing and photography, are being given 

and will continue to be given precedence 

over hunting and fishing. They would like 

to see a balanced program between hunting 

and non-hunting areas.

Several asked how the Refuge will manage 

hunting. Some suggested that the Refuge 

explore how the California Department of 

Fish and Game (DFG) manages hunting 

at other Central Valley refuges. They 

wondered if there is a general agreement 

between DFG and the Service, or if each 

refuge establishes their own arrangement. 

Several attendees said that hunting is 

sustainable and supported by numerous 

organizations. Hunting related purchases 

can help local businesses. Hunters have a 

long tradition of helping with conservation, 

funding and facilities. There were numerous 

references to fees hunters pay to acquire 

and manage habitat through the Duck 

Stamp and Federal excise taxes on hunting 

equipment. Several want to see if some 

of these funds could be earmarked for a 

hunting program or to purchase land for 

hunting at Stone Lakes. They feel the 

Refuge should expand wetlands and increase 

ponds available for hunting. There were 

offers from many hunters to help fund, 

develop, build and monitor hunting facilities. 

There were requests that the Refuge 

develop interpretive materials explaining the 

role of hunters in conservation.

A number of people expressed concern 

over a hunting program. A few mentioned 

hunting related accidents as a cause for 

concern. Some moved to the area to get 

away from places that allow hunting and 

are opposed to it on the Refuge. They 

would like to see the Refuge advance, 

but not at the expense of wildlife. They 

questioned whether hunting is compatible 

with conservation goals and other uses, such 

as education and wildlife viewing. They 

felt that if it is allowed, hunting should not 

occur at the same time as these other uses. 

One group was opposed to both hunting and 

trapping on the Refuge.

Conversely, some said they bought property 

close to the Refuge because of the potential 

public access and the prospect of being 

able to hunt close to home. Many look to 

the Stone Lakes Refuge as the potential 

sole opportunity for public hunting in 

Sacramento County. They want a place 

where they can hunt locally, without having 

to drive a long distance. They expressed a 

need for a hunting program for hunters who 

do not belong to a duck club.

Others were concerned whether there 

are adequate bird populations to support 

observations and hunting and whether 

hunting causes too much disturbance. 

Hunters expressed their hope that the 

Refuge would not be like Cosumnes River 
22 Stone Lakes NWR Comprehensive Conservation Plan

Preserve, which they feel promised hunting 

programs and has failed to provide them.

There was strong consensus on developing 

a junior hunt program; some suggested 

it could be supported by volunteers with 

dogs, time and experience. Several people 

said that a Refuge hunting program should 

not be just exclusively for junior hunters. 

It should also be for adult hunters, both 

beginners and experienced.

The Refuge received many suggestions 

regarding the proportion of land to be used 

for hunting, but most felt that from 40 to 

50 percent of the Refuge should be hunted. 

There was strong interest in splitting access 

between free roam and blind hunting, 

including floating blinds and two to four 

person blinds. There were many requests 

to carefully locate hunt and sanctuary areas. 

Blinds should be accessible to those with 

disabilities. 

People also had suggestions regarding 

how hunting access should occur. Some 

felt that the Refuge should use a lottery/

reservation system and both monitor and 

limit the number of hunters to assure a 

quality hunt. Many cited hunting programs 

at Sacramento, Colusa, Delevan and Gray 

Lodge as models. They would like to see 

adequate facilities, such as good land and 

water access with boat ramps, parking, 

restrooms and other amenities. A request 

was made to allow hunting from scull boats 

and to provide boats to hunters who do no 

have them.

One comment expressed concern that the 

Refuge would serve as a sanctuary and 

draw birds from Yolo (Bypass), negatively 

affecting hunting in Yolo.

Education/Interpretation 

Numerous people commented on the value 

of the Refuge’s educational resources. 

Several programs were noted, such as school 

field trips, events and special projects at 

local schools. Some felt that the primary 

focus of use for the Refuge should be 

educational. They would like to see more 

education programs, including college level 

research projects. The Refuge should work 

with teachers to develop a curriculum and 

teacher/docent training to enhance the 

Refuge visitation experience. It should also 

have a field trip coordinator.

The current limited access and Refuge 

facilities were noted. Comments asked that 

the Refuge develop trails and facilities for 

family use and school field trips. A visitor 

center and signs along trails would help 

students learn about the unique features 

of the Refuge. Having greater access 

to more areas of the Refuge would allow 

more community involvement. The Refuge 

should also consider other outreach sites 

and centers and do what it can to keep these 

activities free.

Several visitor improvements were 

suggested, from a visitor center to new 

interpretive trails. It was suggested that 

the money for these improvements would 

not likely come from Refuge funding, but 

from private fundraising efforts and other 

organizations.

Wildlife Observation

Several comments supported wildlife 

viewing, but stated that the priority must 

be to maintain habitat for wildlife. The 

Refuge should control access to prevent an 

impact on wildlife. They also want to be sure 

that there are no conflicts between wildlife 

observation, hunting and other uses. 

There were several requests for more 

trails, good interpretive signing and specific 

suggestions regarding auto tour routes. The 

Vic Fazio Yolo Basin Wildlife Area auto tour 

route was cited as an example for avoiding 

congestion.

An observation was made that bird watching 

lacks a funding base. Birdwatchers should 

pay a use fee to help cover the costs of 

facilities. A suggestion was made to see 

if money from DFG fines could be used to 

build Refuge facilities. 

A specific comment was made that the 

State Railroad Museum is considering an 

excursion train for wildlife viewing between 
Stone Lakes NWR Comprehensive Conservation Plan 23

the museum and Hood-Franklin Road. We 

should consider a cooperative venture with 

them where our interests overlap.

Other Comments

Comments requested other forms of 

recreational access, such as areas for gun 

dog training and field trials, bicycle access 

on existing roads and trapping fur bearing 

mammals to help reduce the need for a 

predator control program. 

General

A comment was made that the waterways 

need docents to serve as an extra set of 

eyes. Two comments were very supportive 

of the expansion of open space land held 

by public trust agencies and organizations. 

This is particularly so for projects involving 

natural and native habitats, restoration and 

preservation.

Resource issues and opportunities were 

also identified during the scoping process. 

The results of this effort are described in 

Chapter 4, Problems and Opportunities.
24 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 25

3 Refuge Resources

Ecoregion Setting 

Stone Lakes National Wildlife Refuge 

is located in the Central Valley/San 

Francisco Bay Ecoregion. This Ecoregion 

encompasses the Sacramento-San Joaquin 

Delta located within the San Francisco 

Bay-Delta Watershed, with an estuary that 

encompasses roughly 1,600 square miles 

and drains more then 60,000 square miles 

of California’s runoff (SFEP 2000). The 

Delta is composed of 57 leveed islands and 

over 700 miles of sloughs (DWR 2006). The 

Delta includes the confluence of the two 

longest rivers in California, the Sacramento 

and San Joaquin rivers. Following winter 

rains and Sierra snow melt, the Sacramento 

River and its tributaries would historically 

rise above the natural levees and inundate 

the floodplain. This system was dynamic, 

depositing rich alluvium, creating and 

cutting streambanks, providing conditions 

necessary the growth of riparian forests, 

changing the river’s course and creating 

oxbow lakes and backwaters, clearing debris 

and streambeds, exposing and depositing 

gravel and sand, and creating salmonid 

spawning habitat. Toward the Delta, 

with the greater influx of sediment, more 

substantial natural levees were deposited 

where larger, more diverse riparian forests 

occurred (Katibah 1984). 

Flyway Setting 

The Refuge is located within the Pacific 

Flyway. The Pacific Flyway is used by 

millions of waterfowl and shorebirds 

for migration to wintering and breeding 

grounds. This Refuge is an important 

stopover area for migrating shorebirds in 

the fall and spring and provides important 

wintering habitat for waterfowl, supporting 

approximately 60 percent of the total 

population (CVJV 1990).

Natural/Historic Conditions 

Historically the Central Valley supported 

about four million acres of wetlands with 

associated grasslands and riparian areas 

(CVJV 1990). Permanent and seasonal 

wetlands provided wintering and breeding 

habitat for waterbirds and other wildlife 

that flourished through the region. Prior to 

large scale disturbance, natural processes 

dominated the area. The Stone Lakes Basin 

is located within the 100-year floodplain. 

Historically, periodic floods would sweep 

through the area changing the course of the 

rivers and waterways and resetting natural 

community succession in the area. In 

addition, fire was a regular component of the 

area’s ecosystem, sweeping through the area 

every three years. 

The 1992 EIS (USFWS 1992) identified the 

location and extent of historic wetlands in 

the Refuge planning area, based on U.S. 

Geological Survey (USGS) atlas sheets of 

the Sacramento Valley surveyed in 1903-

1910. Before 1903, activities related to flood 

control, water conveyance, and agricultural 

conversion had already reduced the extent 

of wetlands prior to the survey. The NRCS, 

formerly the Soil Conservation Service, 

mapped locations of hydric soils in 1990 that 

are generally assumed to correspond to the 

locations of historic wetlands. 

Most of the open water, wetland, and 

riparian areas present on the Refuge in 1910 

have since been drained and converted to 

agricultural uses. Today, over 95 percent 

of the riparian habitat in the Central Valley 

has been destroyed due to agricultural 

expansion and urbanization. Beach Lake 

and its associated wetland and riparian 

vegetation covered a much larger area 

before it was drained and farmed as recently 

as the 1960s (Figure 4) (USFWS 1992). 
26 Stone Lakes NWR Comprehensive Conservation Plan

North Stone Lake, which is similar in size to 

its historic extent, had been drained, cleared 

and farmed prior to World War II. South 

Stone Lake was originally about three times 

its present size extending well west of the 

former Southern Pacific Railroad levee that 

now forms its western boundary. 

An extensive area of freshwater wetlands 

1.0 - 1.5 miles wide, was present in overflow 

areas east of Snodgrass Slough and between 

Snodgrass Slough and the Mokelumne River. 

Bear Lake, a narrow lake more than two 

miles long located between Lambert Road, 

Twin Cities Road, Snodgrass Slough and the 

railroad, no longer exists.

Overflow areas of the Cosumnes River 

supported extensive freshwater wetlands, 

about 1 mile wide, upstream of Grizzly 

Slough and downstream of Twin Cities Road. 

An unnamed lake about 1.5 miles long and 

1,000 feet wide located east of Bruceville and 

west of the Cosumnes River, was drained 

and converted to agricultural land. 

Little historical data is available that 

describes waterfowl use of the Refuge. 

However, maps of the Refuge developed 

by USGS prior to 1910 indicate that large, 

tidally influenced, permanent and seasonal 

wetlands existed, especially in the southern 

portion of the Refuge toward the Cosumnes 

River and at Beach, North Stone and South 

Stone lakes. These wetlands undoubtedly 

attracted large numbers of swans, geese, 

ducks and other waterbirds. Levee 

construction and channelization of rivers, 

creeks and other natural drainages and 

conversion of floodplains to agriculture have 

largely reduced the numbers of breeding 

and wintering waterfowl the Refuge can 

support. Historically, ducks were likely 

more abundant on the Refuge than they are 

at present (USFWS 1992). Local residents 

reported successful private duck hunting at 

South Stone Lake and the farmlands near 

Hood-Franklin and Lambert Roads from 

the 1940s until the early 1960s (USFWS 

1992). Duck hunting at South Stone Lake 

was marginal by the early 1960s and has 

continued to decline during the last three 

decades (USFWS 1992).

Geographic and Physical Setting 

Topography

The Refuge is part of a fairly level, but 

undulating, ancient alluvial plain incised 

by Morrison Creek, the Cosumnes River 

and several small creeks. Morrison 

Creek traverses the northern portion of 

the Refuge. The land slopes west to the 

Sacramento River. Elevations on the Refuge 

range from near mean sea level to 25 feet 

above mean sea level. Several small creeks 

traverse the western and northwestern 

portions of the Refuge. 

While much of the Refuge was laser leveled 

in the past for agriculture, portions of it, 

particularly in the North Stone Lake area, 

still have their native undulating topography. 

Geology

The Refuge is within the Great Valley 

Physiographic Province. The dominant 

geologic structure is the northwest to 

southeast-trending asymmetrical syncline 

that underlies the valley. A syncline is a fold 

in the rocks of the Earth’s crust in which 

the layers or beds dip inwards, thus forming 

a trough like structure with a sag in the 

middle.

The Refuge is underlain by materials 

comprised of quaternary alluvial and 

intertidal depositions. Most of the Refuge 

is underlain by the Victor formation. The 

Victor alluvial formation was deposited in 

the late Pleistocene (about one million years 

ago) by materials washed from the Sierra 

Nevada. During the mid-Holocene era, 

about 5,000 years ago, basin, intertidal, levee 

and channel deposits accumulated along 

the Sacramento and Cosumnes rivers. The 

Victor formation consists of poorly sorted 

alluvial materials that vary in size from clays 

to boulders. Erosion of the Victor Formation 

has led to accumulation of finer grained 

basin deposits along the Sacramento and 

Cosumnes rivers near the Delta. Intertidal 

deposits of soft mud and peat accumulated 

west of Snodgrass Slough at the margin of 

the Delta. More recently, natural levee and 

channel deposits have accumulated along the 

Sacramento and Cosumnes rivers.
Stone Lakes NWR Comprehensive Conservation Plan 27

Sacramento River

160

99

104

5

North

Stone

Lake

Twin Cities Rd

Snodgrass Slo u gh

SP Cut Elliot Ranch Rd

Lambert Rd

Elk Grove Blvd

Hood Franklin Rd

To Stockton

To Sacramento

Franklin Blvd.

Sacramento

Regional

Wastewater

Treatment

Plant

South

Stone

Lake

Southern Pacific Railroad (abandoned)

Beach

Lake

Unit

Wetland

Preserve

Unit North Stone

Lake Unit

HQ

Unit

South

Stone

Lake

Unit

Stone Lakes

National Wildlife Refuge

Figure 4. Refuge Unit Names and Roads

0 0.5 1 2

Miles

0 0.5 1 2 Kilometers

Approved Refuge Boundary

Non-Refuge Lands

Beach Lake Unit

HQ Unit

North Stone Lake Unit

South Stone Lake Unit

Wetland Preserve Unit

Refuge Headquarters
28 Stone Lakes NWR Comprehensive Conservation Plan

Soils

Two systems are used by the NRCS to 

describe the Refuge soils: general soil map 

units and detailed soil series. The general 

soil map units represent broad patterns of 

the soil, topographic relief and drainage 

classes. Typically, each general soil map 

unit consists of one or more soil series. The 

general soil map can be used to compare the 

suitability of large areas for general land use 

(USFWS 1992). Soil series maps provide the 

finer level of detail necessary for site specific 

planning.

Refuge soils can be classified into three 

general soil types. 

• Egbert Clays and Valpac Loams

• Dierssen sandy clay loams and clay 

loams

• Clear Lake Clays

Along the Sacramento River, the soils are 

characteristically very deep and nearly 

level. These soils are in the floodplain and 

originally supported extensive wetland 

and riparian habitats. The Egbert-Valpac 

general soil type forms a continuous one 

mile wide strip along the Sacramento River 

and Snodgrass Slough. It is comprised of 

somewhat poorly drained soils in areas with 

a high water table either throughout the 

year or seasonally. Prime farmland soils 

with high fertility are generally found in 

Egbert-Valpac general soil units. 

The dominant general soil on the Refuge 

is Dierssen. Dierssen map units are 

comprised of somewhat poorly drained soils 

in areas with a perched water table and are 

moderately deep to deep over a cemented 

hardpan. Clear Lake soils, which are 

present in small areas east of the Dierssen 

soil unit, are also somewhat poorly drained 

and underlain by a shallow cemented 

hardpan. They have a seasonally high water 

table perched above the hardpan. Both the 

Dierssen and Clear Lake general soil map 

units are nearly level and are found in basins 

and on basin rims. Both areas are protected 

by flood control levees.

Clays are the most dominant soil particle 

on the Refuge; thus soils tend to be hydric. 

Hydric soils correspond to historic locations 

of wetlands and open water bodies, forming 

under frequent water saturation and the 

resulting anaerobic soil conditions. Silty 

and/or sandy soil belts are interspersed and 

are identifiable by the associated vegetation. 

Soils on the Refuge have been divided into 

soil mapping units. A total of 30 soil map 

units are found on the Refuge. These map 

units were used in the EIS (USFWS 1992) to 

predict the best areas for restoration. 

Climate

The Refuge lies between the Coast and 

Diablo Ranges to the west and the Sierra 

Nevada to the east. The Carquinez Strait 

provides a sea-level gap between the 

Coast Ranges and the Diablo Range. The 

Carquinez Strait is about 55 miles southwest 

of the Refuge and the intervening terrain is 

mainly flat with rolling hills. The prevailing 

winds blow from the south, primarily due 

to marine breezes through the Carquinez 

Strait. During winter, the sea breezes 

diminish and winds from the north occur 

more frequently. However, winds from the 

south still predominate. The climate in the 

Refuge area is temperate and semiarid, with 

hot, dry summers and cool, damp winters. 

Annual temperatures in the area average 

highs of 52 degrees Fahrenheit in January 

to about 93 degrees Fahrenheit in July and 

lows of 38 degrees Fahrenheit in January 

to 58 degrees Fahrenheit in July. Annual 

precipitation averages about 17 inches. 

Dense “tule” fog is common in winter 

(USFWS 1992).

Air Quality

Air Pollution Control Agencies. The 

Federal Clean Air Act (42 U.S.C. §§ 7401, 

as amended) mandates the establishment 

of ambient air quality standards and 

requires areas that violate these standards 

to prepare and implement plans to achieve 

the standards by certain deadlines. The 

deadline for attaining both the ozone and 

carbon monoxide (CO) standards was 

August 31, 1988. Areas that do not meet 

Federal primary air quality standards 

are designated as “nonattainment” areas. 

Areas that comply with Federal air quality 

standards are designated as “attainment” 
Stone Lakes NWR Comprehensive Conservation Plan 29

areas. Attainment and nonattainment 

designations are pollutant specific. Thus, 

while Sacramento County is a nonattainment 

area for particulate matter less than 10 

microns in diameter (PM10) and ozone it 

is an attainment area for carbon monoxide 

(CO), nitrogen oxide (NOx), sulfur dioxide 

(SO2) and lead.

Many agencies are involved in air pollution 

control, including the U.S. Environmental 

Protection Agency (USEPA 2006), California 

Air Resources Board (ARB), Sacramento 

Metropolitan Air Quality Management 

District (SMAQMD) and other air quality 

management districts (AQMDs). 

In California, all agricultural burning is 

regulated jointly by the ARB and local 

AQMDs. Each day the ARB determines, 

based on recent and anticipated weather 

conditions, whether the following day will 

be a permissible burn day or a no-burn day. 

Each ARB’s primary objective in making 

this determination is to control the amount 

of smoke from agricultural burning that 

reaches urban areas. On permissible burn 

days, few restrictions are placed on the 

amount of land that may be burned in the 

region. On no-burn days, fields may be 

burned only if a special permit has been 

issued by the local AQMD. Such burn 

permits are allocated based on an estimated 

allowable acreage for the entire region.

Ambient Air Quality Standards and 

Existing Air Quality in Sacramento 

County

Both the State of California and the Federal 

government have established a variety of 

ambient air quality standards. The following 

discussion focuses on the ambient standards 

and existing concentrations for PM10, 

ozone and CO for two reasons: Sacramento 

County’s air quality currently exceeds the 

allowable ambient standards for PM10 and 

ozone and these pollutants, together with 

CO, are the primary pollutants that could be 

affected by the Refuge.

PM10. Health concerns associated 

with suspended particles focus on those 

particles small enough to reach the lungs 

when inhaled. Few particles larger than 

10 microns in diameter reach the lungs. 

Consequently, both the Federal and State 

air quality standards for particulate matter 

have been recently revised to apply only to 

these small particles (designated as PM10).

The entire Sacramento Valley, including 

Sacramento County, is classified as a PM10 

moderate nonattainment area (USEPA 

2006). Both the 24 hour and annual 

California PM10 standards are violated 

on a regular basis in the Sacramento area 

(USFWS 1992). Sacramento County PM10 

emissions are generated by a variety of 

sources, primarily entrained road dust, 

construction and demolition activities. 

Farming operations and agricultural waste 

burning are also important sources of PM10 

in Sacramento County. 

Ozone. Ozone is a respiratory irritant that 

also increases susceptibility to respiratory 

infections. Ozone causes substantial damage 

to leaf tissues of crops, natural vegetation 

and damages many materials by acting as a 

chemical oxidizing agent.

The Federal air quality standard for 

ozone is exceeded several times a year at 

monitoring stations in Sacramento County. 

As a consequence of the recorded violations 

of the Federal ozone standard, the entire 

Sacramento Valley Air Basin, including 

Sacramento County, has been designated 

a serious nonattainment area of ozone 

(USEPA 2006). This indicates that the ozone 

levels in the Sacramento Valley air basin are 

a potential threat to public health. Human 

health effects of ozone can include difficulty 

breathing and lung tissue damage (ARB 

2006).

Ozone, the main component of photochemical 

smog, is primarily a summer and fall 

pollution problem. Ozone is not emitted 

directly into the air but is formed through 

a complex series of chemical reactions 

involving other compounds that are directly 

emitted. These directly emitted pollutants, 

also known as ozone precursors, include 

reactive organic gases (ROG) and NOx

(ARB 2006). The period required for ozone 
30 Stone Lakes NWR Comprehensive Conservation Plan

formation allows the reacting compounds 

to be spread over a large area, producing a 

regional pollution problem. Ozone problems 

are the cumulative result of regional 

development patterns, rather than the result 

of a few significant emission sources. Motor 

vehicles are the primary source of NOx and 

ROG in Sacramento County and therefore, 

are primary contributors to regional ozone 

concentrations.

Carbon Monoxide (CO). CO combines 

readily with hemoglobin and thus reduces 

the amount of oxygen transported in the 

bloodstream. Relatively low concentrations 

of CO can meaningfully affect the amount of 

oxygen in the bloodstream because CO binds 

to hemoglobin 220-245 times more strongly 

than oxygen. Both the cardiovascular 

system and the central nervous system can 

be affected when 2.5 percent to 4.0 percent 

of the hemoglobin in the bloodstream is 

bound to CO rather than to oxygen. State 

and Federal ambient air quality standards 

for CO have been set at levels intended to 

keep CO from combining with more than 

1.5 percent of the blood’s hemoglobin (U.S. 

EPA 1978, California ARB 1982).

Sacramento County has been designated as 

a nonattainment area for CO in the past, but 

is no longer considered a nonattainment area 

(USEPA 2006). Motor vehicle emissions are 

the dominant source of CO in most areas. 

As a directly emitted pollutant, CO disperses 

as it is transported away from the emission 

source, reducing pollutant concentration. 

Consequently, CO problems are usually 

localized, often the result of a combination of 

high traffic volumes and traffic congestion. 

Data from previous studies suggest that CO 

problems occur primarily near major traffic 

arteries having large amounts of commercial 

development. The Refuge is located on 

either side of Interstate-5 adjacent to and 

within the Sacramento urban area.

CO is primarily a winter problem. High CO 

levels develop primarily during winter when 

periods of light winds or calm conditions 

combine with the formation of ground 

level temperature inversions (typically 

in the evening through early morning 

period). These conditions result in reduced 

dispersion of vehicle emissions, allowing 

CO problems to develop and persist during 

hours when traffic volumes are declining 

from peak levels. It is unknown how 

elevated CO levels affect Refuge resources. 

Motor vehicles also exhibit increased CO 

emission rates at low air temperatures 

(USFWS 1992).

Contaminants and Water Quality 

Water sources within the Refuge boundary 

include Morrison and Laguna creeks, Upper 

and Lower Beach lakes, urban runoff and 

agricultural drainage, Southern Pacific Cut 

(SP Cut), North and South Stone lakes and 

groundwater. Water quality monitoring 

by the SRCSD and the Service have been 

completed to date on the Refuge and in the 

surrounding area. 

Water quality in North and South Stone 

Lakes is affected by limited Delta and San 

Joaquin River daily tidal flows moving up 

Snodgrass Slough through the Lambert 

Road bridge water control structure. 

Agricultural activities upstream of lakes may 

influence water quality from direct drainage 

into the lakes and the SP Cut. Groundwater 

discharge/recharge and Mokelumne River 

upflow via Snodgrass Slough to and from 

the lakes may also influence water quality in 

the lakes. The SRWTP does not discharge 

effluent into the Morrison Creek watershed. 

Instead, the treated effluent is dechlorinated 

and discharged directly to the Sacramento 

River near the community of Freeport.

The Refuge has many drainages that 

originate in urban and agricultural areas and 

empty into Refuge wetlands and lakes. In 

addition, a significant portion of land within 

the approved Refuge boundary is currently 

in agriculture. These areas are likely 

sources of nonpoint source contaminants, 

however they also provide important habitat 

for fish, aquatic invertebrates and foraging 

areas for birds that feed on these resources. 

Monitoring of aquatic habitats for nonpoint 

pollution is important, especially on this 

Refuge which is surrounded by urban 

development and actively managed 

agriculture.
Stone Lakes NWR Comprehensive Conservation Plan 31

The Sacramento Regional Wastewater 

Treatment Plant conducts ongoing quarterly 

water sampling for certain trace elements 

at several locations along Morrison 

Creek, Laguna Creek, and Meadowlark 

and Black Crown lakes. Furthermore, 

the USACE sampled water from the 

Morrison Creek watershed from 1982 to 

1984. Concentrations of cadmium (Cd), 

copper (Cu) and lead (Pb) exceeded the 

USEPA acute toxicity criterion for aquatic 

life in all samples. The DFG and SWRCB 

collected and analyzed largemouth bass 

(Micropterus salmoides) from Meadowlark 

Lake from 1985 – 1987 and analyzed for 

heavy metals and organochlorine pesticides 

(OCs). Elevated levels of mercury (Hg), 

Cu, chlordane, dacthal, total DDT and total 

polychlorinated biphenyls (PCBs) were 

detected. Environmental contaminants are 

clearly present in the Stone Lakes area, but 

have been poorly delineated. 

Baseline sampling on the Refuge and in 

nearby areas was conducted by the Service 

in 1997. The Service collected water, 

sediments, crayfish, fish, and waterbird 

eggs and analyzed them for OCs, PCBs 

and trace elements. Generally low levels 

of trace elements were found in water and 

biota, and generally low levels of organic 

compounds were present in sediments 

and biota. Concentrations of certain trace 

elements exceeded the USEPA’s threshold 

effects level in sediments. Concentrations 

of trace elements were consistently higher 

(relative to other sites) in sediments from 

Lower Beach Lake. Lower Beach Lake is 

the terminus of Morrison Creek and may 

accumulate contaminants that originate in 

the greater Sacramento metropolitan area. 

Further sampling and toxicity tests of water 

and sediments are needed to identify the 

source of the contamination in Lower Beach 

Lake and other nearby areas (USFWS 

2003a).

Water, sediment and biota samples were 

collected from eight locations (three sites 

in Morrison Creek, two sites in North 

Stone Lake and three sites in South Stone 

Lake) in spring on 1997 (Thomas 1997). 

Samples were analyzed for dissolved 

oxygen, temperature, heavy metals 

(arsenic, cadmium, copper, lead, mercury, 

selenium and zinc), salts (sodium chloride, 

calcium ion and magnesium), Nitrate NO3

and pH. Results indicate that levels of 

heavy metals, although present, were not 

sufficient to cause deleterious impacts to 

wildlife; concentrations of selenium in all 

five waterbodies tested are above levels 

recommended for the protection of aquatic 

life. 

Additional sampling was conducted 

from December 1998 to January 2000 on 

stormwater runoff onto the Refuge. The 

water quality of the Refuge and surrounding 

areas is continuously being degraded by 

irrigation drainwater and urban drainage in 

the summer, and the flushing of accumulated 

pollutants via urban stormwater runoff 

in the winter. Water samples and water 

quality data (temperature, dissolved oxygen, 

conductivity and pH) were collected from 

11 sites on the Refuge during four storm 

events from December 1998 to January 

2000. Temperature, pH, dissolved oxygen 

and conductivity were within normal limits 

for all sites, except for dissolved oxygen 

at Morrison Creek, which was at or below 

3.0 milligrams/liter (mg/L) during two of 

the storm events. Overall, trace element 

concentrations in stormwater entering the 

Refuge were relatively low. Seven of 16 

trace element samples collected during the 

two storm events had copper concentrations 

above the hardness adjusted chronic 

criterion and of those, three were also above 

the acute criterion. Four of 16 samples 

had lead concentrations above chronic 

criterion. Only one sample out of 16 had 

a concentration of cadmium that would be 

considered significantly elevated above the 

hardness adjusted chronic criterion (3.75 

times the criterion). Nearly all sites had 

Diazinon levels above DFG’s proposed 50 

mg/L chronic criterion; however, they did 

not all produce measurable toxicity when 

daphne (Ceriodaphnia dubia) were exposed 

to the samples. Two sites, one on the Lower 

Beach Lake Unit and another that flows into 

Lower Beach Lake, consistently showed 

levels of Diazinon that produced toxicity to 
32 Stone Lakes NWR Comprehensive Conservation Plan

Ceriodaphnia along with detectable levels 

of chlorpyrifos. Concentrations of Diazinon 

at these sites ranged from 101 to 1,488 mg/L 

with measured toxicity units ranging from 

3.2 to 3.5 (USFWS 2003b).

Sacramento County’s National Pollutant 

Discharge Elimination System (NPDES) 

Municipal Permit requires that pollutants 

found in urban stormwater runoff be 

reduced to the maximum extent possible. 

Dry detention stormwater runoff treatment 

facilities were constructed as part of the 

3,000-acre development east of the Refuge 

identified in the East Franklin Specific 

Plan and would likely be included in other 

projects as well. These detention basins are 

effective in reducing pollutants by 30 to 90 

percent.

Discharge Water Quality Monitoring

The Central Valley Regional Water 

Quality Control Board (Regional Board) 

issued order No. R5-2006-0054, regulating 

discharges from irrigated lands, effective 

beginning July 1, 2006 and ending June 30, 

2011 (CVRWQCB-CVR 2006). The order 

detailed an individual discharger conditional 

waiver of waste discharge requirements. 

The order states that individual dischargers 

can seek coverage under the Individual 

Discharger Conditional Waiver or under 

the Coalition Group Conditional Waiver, by 

joining a coalition group. The conditional 

waiver requires Dischargers to pay a fee to 

the State Water Board. The Water Quality 

Control Plan for the Central Valley Region 

designates beneficial uses and establishes 

water quality objectives (CRWQCB-CVR 

2004). 

During the development of the irrigated 

lands waiver the Regional Board included 

discharges from “managed wetlands” in the 

definition of irrigated lands (USFWS 2004). 

However, the term “managed wetlands” is 

not defined by the Regional Board. There 

is a broad range of management activities 

that occur on Refuge wetlands. Some forms 

of management are relatively passive while 

others are very intensive due to enhance 

habitat for endangered and threatened 

species as well as migratory birds. 

During the development of the waiver, the 

Service objected to being included under the 

waiver and recommended that a separate 

waiver be developed for managed wetlands. 

The Regional Board recognized that wetland 

discharges were sufficiently different than 

agriculture and a separate waiver would be 

appropriate but they did not have sufficient 

funds and staff to develop a separate waiver 

at the time. Thus the Regional Board’s 

irrigated lands waiver and its requisite 

monitoring programs are primarily 

designed to address pesticide discharges 

from agriculture and does not take into 

consideration the differences and uniqueness 

of wetlands.

Meeting the waiver requirements is at best 

awkward for wetland managers, including 

the Refuge, because the irrigated lands 

waiver is designed to address discharges 

from irrigated agriculture. In evaluating 

the irrigated lands waiver requirements, 

the Service believes that the monitoring 

requirements for an individual discharger 

under the waiver are more appropriate 

for wetland discharges. They require 

monitoring of pesticides and toxicity only if 

certain chemicals or pollutants of concern 

are discharged, whereas the primary 

monitoring program for coalitions requires 

monitoring of all pollutants of concern since 

a coalition is more likely to represent a 

large variety of pesticide uses and discharge 

types.

The Refuge manages seasonal and 

permanent wetlands on the South Stone 

Lake, Headquarters and Beach Lake Units 

totaling approximately 335 acres. Periodic 

draw downs of the permanent wetland 

impoundments on the Beach Lake Unit 

is done when vegetation, such as cattails, 

covers more than 75 percent of the wetland 

and to control weeds and undesirable fish 

species, such as carp. During years with 

no restrictions on water use, flood ups of 

seasonal wetlands begin in early to midSeptember and continue through late 

fall depending on rainfall. Drawdowns 

commence in early April and continue 

through mid-June. Seasonal wetland 
Stone Lakes NWR Comprehensive Conservation Plan 33

drawdowns are accomplished through a 

combination of evaporation and opening 

of water control structures. Depending on 

annual rainfall, flood waters are pumped 

out of the Sun River property of the South 

Stone Lake Unit to minimize damage to 

infrastructure and facilitate draw downs. 

Supplemental summer irrigation of seasonal 

wetlands to stimulate desirable plant growth 

for migrating waterfowl is done in late July 

and early August to a maximum depth of 12 

inches for 24 hours and then drawndown by 

opening water control structures within a 

few days. 

Only one type of discharge to waters of the 

State, as defined in Regional Board order 

No. R5-2006-0054, occurs on the Refuge: 

storm water runoff from the Refuge during 

flooding events. Discharge to waters of 

the State is defined by order No. R5-

2006-0054 as “Surface discharges, such as 

irrigation return flows, tailwater, drainage 

water, subsurface drainage generated 

by irrigating crop land or by installing 

and operating drainage systems to lower 

the water table below irrigated lands 

(tile drains), stormwater runoff flowing 

from irrigated lands, stormwater runoff 

conveyed in channels or canals resulting 

from the discharge from irrigated lands, 

and/or operational spills containing waste” 

(CVRWQCB-CVR 2006). See “Current 

Management Practices: Wetlands” in 

Chapter 3 for a detailed discussion of Refuge 

wetland management practices.

Pesticide Use and Toxicity Testing

The Service does not propose to do toxicity 

testing of its wetland discharges. All 

pesticide use on the Refuge, is part of an 

Integrated Pest Management (IPM) plan 

and adheres to pesticide label instructions, 

Intra-Service Section 7 Consultations under 

the Endangered Species Act, Sacramento 

County pesticide bulletin protective 

measures for threatened and endangered 

species, buffer requirements and other 

appropriate best management practices.

Since the mid-1990s, the Refuge has 

collaborated with a number of private, local 

and state entities as a participant in the 

Stone Lakes Basin Water Hyacinth Control 

Group (SLBWHCG). As a result of water 

hyacinth control efforts to date, the extent 

of plant infestations has been reduced to an 

estimated 30 to 35 acres. With continued 

applications, it is anticipated that beyond 

2006, control efforts may be scaled back 

to occasional treatments (two to three per 

week) during the hyacinth growing season to 

spot-treat small infestations. 

The Stone Lakes Basin water hyacinth 

control program is permitted under a 

Statewide National Pollution Discharge 

Elimination System (NPDES) General 

Permit (No. CAG990005) for discharge of 

aquatic pesticides. Field crews with the 

Service and the SRCSD conduct chemical 

control of water hyacinth on approximately 

670 acres of open water habitats on Lower 

Beach Lake, SP CUT (the borrow channel 

for the former Southern Pacific Railroad), 

North Stone Lake and South Stone Lake 

and its tributaries. Control activities occur 

in natural lakes and sloughs as well as 

man-made irrigation or drainage ditches 

and channels. Treated waterways lie within 

lands owned by the Service, the State 

of California, Sacramento County and 

a number of private landowners. Since 

infestations of water hyacinth within the 

Basin have been greatly reduced due to 

past efforts, it is anticipated that a steadily 

decreasing quantity of herbicide will be 

needed as the program becomes more of a 

maintenance operation. To comply with the 

monitoring and reporting requirements of 

the NPDES General Permit, the Refuge 

and SRCSD provide an annual report to the 

California Regional Water Quality Control 

Board summarizing aquatic pesticide 

applications and the results of water quality 

monitoring for the water hyacinth control 

program. 

The Refuge also cooperates with 

Sacramento-Yolo Mosquito Vector Control 

District (SYMVCD) to mitigate the risk of 

mosquito borne diseases. See Appendix 

A, Compatibility Determination for 

Monitoring and Control of Mosquitoes 

for detailed information. The SYMVCD 

and the Service rely on a full range of 
34 Stone Lakes NWR Comprehensive Conservation Plan

IPM techniques to manage mosquito 

populations, including wetland design 

features, water and vegetation management, 

biological control and chemical control of 

larval or adult mosquitoes. As a result 

of IPM practices larvicide applications 

on the Refuge have been limited to small 

acreages and adulticides have historically 

been used infrequently (i.e., three ground 

ultra-low volume applications during 10 

years). Largely due to the 2005 detection 

of West Nile Virus, the Refuge received 

ground ultra-low volume applications of 

the adulticide pyrethrin on 18 occasions in 

2005 and six applications to date in 2006. 

Additional applications of adulticides are 

likely during the remainder of the 2006 

season. .

Since the majority of Refuge uplands are 

not irrigated they do not technically fall 

under the irrigated lands waiver. The IPM 

methods that the Refuge uses to control 

weeds include burning, mowing, discing and 

application of herbicides including Roundup 

(glyphosphate) and 2, 4-D. Multiple 

treatments on the same acreage in one year 

are rare and are usually spot applications. 

Also, since these are Refuge uplands, 

virtually all areas where applications occur 

have vegetated buffers between applications 

and any waterbodies.

While irrigated agriculture is conducted 

within the approved Refuge boundary, it is 

not conducted on lands under the control 

(i.e., fee title ownership, cooperative 

management agreement, conservation 

easement) of the Refuge. While 

participating in a watershed monitoring 

coalition group with adjacent irrigated 

agricultural producers is a possible option, 

discharge from adjacent agricultural lands, 

not managed by the Service, is ultimately 

the responsibility of the discharger. 

The Refuge, by policy and mandate, 

is managed utilizing many of the best 

management practices to reduce pesticide 

and fertilizer runoff, they are considered 

the basic elements of good refuge habitat 

management. Refuge policy mandates 

limited use of pesticides only after physical 

or other means (e.g., controlled burns, 

grazing, mowing) are used and after review 

and approval by management. Most 

herbicide treatments are a part of longterm habitat restoration and management 

plans on uplands where treated areas are 

being restored to native habitat. Except for 

approximately 490 acres of irrigated pasture 

land, Refuge uplands are not irrigated. 

All applications of herbicides on Refuge 

uplands occur where there are natural 

vegetated buffers from aquatic habitats. 

Many riparian areas have understory 

vegetation that minimizes potential drift into 

waterbodies. Also, aerial applications are 

not utilized on the Refuge. Applications for 

upland weeds are typically spot treatments 

of discrete stands of plants and multiple 

applications on the same acreage in one year 

are rare . For these reasons the Service 

does not propose to do toxicity testing of its 

wetland discharges.

Pesticide Monitoring

The Refuge and SRCSD will continue 

monitoring of water quality required 

under the NPDES General Permit for the 

application of aquatic herbicides for the 

water hyacinth control program. Given 

that minimal discharge, if any, occurs 

from the Refuge and that water quality 

monitoring is already occurring, the Refuge 

intends to file as an individual discharger, 

under the Central Valley Regional Water 

Quality Control Board’s, Irrigated Lands 

Conditional Waiver for water dischargers.

Water Quality is further discussed in 

Chapter 4.

Hydrology 

The Refuge lies within the Beach-Stone 

Lakes Basin in the northeast portion of 

the Sacramento-San Joaquin Delta. This 

Basin is within the lower watershed of 

the Morrison Creek drainage, with the 

Sacramento River to the west and the 

Mokelumne and Cosumnes rivers nearby 

to the southeast (Figure 1). The lower 

Morrison Creek watershed governs the 

surface water flow patterns over the Refuge. 

This 180-square-mile system of streams and 
Stone Lakes NWR Comprehensive Conservation Plan 35

floodplain originates in eastern Sacramento 

County and includes portions of the City of 

Sacramento, Morrison, Unionhouse, Laguna, 

Elk Grove and Elder creeks. Streamflows in 

these channels are affected by storm runoff, 

springs, urban drainage, groundwater 

pumping for irrigation, water supply and 

diversions and surface storage ponds located 

throughout the watershed. Waters on the 

Refuge are also influenced by the Cosumnes 

and Mokelumne rivers, especially during 

floods when water from the two rivers backs 

up the Southern Pacific Railroad borrow 

canal (SP Cut).

The Morrison Creek stream group drains 

a large urban and agricultural watershed 

that includes Laguna and, Morrison 

creeks and Beach Lake. Many commercial 

and industrial sources contribute runoff 

to Morrison Creek. Most streams are 

intermittent and historically dry during 

the summer. Today, urbanization and 

agricultural practices in this watershed have 

resulted in low summer flows consisting of 

runoff from irrigation, wastewater flows and 

agricultural return flows (USFWS 1992).

Elevations in the Morrison Creek watershed 

range from 300 feet above mean sea level 

(MSL) in the northeast and slope gently 

down to sea level in the Beach-Stone Lakes 

Basin in the southwest. Construction of a 

reclamation district levee before the turn of 

the twentieth century divides Upper Beach 

Lake, which extends northeastward under 

Interstate-5, from Lower Beach Lake. This 

levee directs water draining down Morrison 

Creek from Upper Beach Lake to an electric 

pump (City Sump 90) that discharges it 

directly into the Sacramento River near the 

town of Freeport. 

During winter high-flow periods when 

Upper Beach Lake rises 3 feet above MSL, 

water overtops the dike dividing Upper 

and Lower Beach Lake and spills into 

Lower Beach Lake and the Southern Pacific 

railroad borrow ditch (SP Cut). Water 

then continues south to North Stone Lake, 

Hood-Franklin Road and South Stone Lake; 

passes through the Lambert Road Bridge 

flood control structure; and then enters 

Snodgrass Slough. Snodgrass Slough 

provides a surface hydrologic connection for 

the Basin and the Sacramento-San Joaquin 

Delta near the town of Locke (Jones and 

Stokes Associates 1989). Nearly all the 

lands within the approved Refuge boundary 

are within the 100-year floodplain.

Also see Chapter 4, Hydrology.

Water Supply 

Water sources available for maintenance 

and management of Refuge fish and wildlife 

habitats and irrigation include: runoff from 

local sources such as the Morrison Creek 

drainage, shallow groundwater and surface 

flows from Snodgrass Sough. Surface 

flows from direct precipitation and surplus 

irrigation returns within the Beach-Stone 

Lakes Basin provide water sources for 

habitats and farming operations adjacent to 

the SP Cut. The Basin and SP Cut are also 

used as a tailwater and stormwater runoff 

drain for reclamation districts lying to the 

west. 

Interception of shallow groundwater is used 

to sustain habitats and agricultural lands 

within the Refuge and the Beach-Stone 

Lakes Basin. Due to irrigation withdrawals, 

there is a groundwater depression in the 

water table south and east of the Refuge 

area. This groundwater depression creates 

a gradient away from the Sacramento River 

and locally induces flow from the river across 

the Refuge area toward the center of the 

depression. Therefore, groundwater that is 

intercepted by channels and wells within the 

Beach-Stone Lakes Basin is likely seeping 

from the river. 

In response to the daily tidal cycle, water 

levels in Snodgrass Slough and the SP Cut 

are influenced by operation of a slide gate 

and flap gates on the Lambert Road Bridge 

flood control structure; diversion of water 

by various upstream users, including the 

Refuge and operation of the Delta Cross 

Channel by the California Department 

of Water Resources for the State Water 

Project. South to north flows of surface 

water occur through the Lambert Road 

Bridge flood control structure and these 
36 Stone Lakes NWR Comprehensive Conservation Plan

reverse flows play a substantial role in 

sustaining the water supply in the BeachStone Lakes Basin. 

Biological Resources

Plant Communities 

Vegetation communities are categorized 

below as grassland, riparian, woodland 

or wetland (Figure 5. Vegetation Map). 

Agricultural crops, vineyards, and urban 

developments are only addressed on the 

Vegetation Map.

Grasslands. Grasslands on the Refuge 

are broken into three categories: annual 

grassland, perennial grassland and irrigated 

pastures. Grasslands are open habitats 

supporting grasses and forbs with little or 

no woody vegetation. The gently rolling 

terrain surrounding North Stone Lake 

is covered with large areas of annual 

grasslands mixed with seasonal wetlands.

Annual. Most of the grasslands in 

California are dominated by annual, 

nonnative grasses and forbs as a result of 

cultivation, livestock grazing, changes in 

fire regimes and other disturbances (Heady 

1988). Characteristic species include the 

dominant species, wild rye (Lolium sp.), 

as well as wild oats (Avena fatua), bromes 

(Bromus spp.) and filarees (Erodium spp.). 

Some annual grasslands are interspersed 

with native perennial grasses and forbs. 

Restoration and management are a focal 

part of grassland management for native 

grasses and forbs, such as creeping wild 

rye and California poppy (Eschscholzia 

californica), as well as many other species. 

The grazing regime is the primary tool, used 

by managers, to enhance native grassland 

species; however, prescribed burning, water 

manipulations, mowing and discing are also 

utilized. See the section on “Grasslands” 

under “Current Management” later in this 

chapter for more information. 

Perennial. Before Euroamerican 

settlement, most of the Central Valley 

grassland was dominated by native purple 

needlegrass (Nassella pulchra). Open 

areas between the tussocks of this perennial 

bunchgrass supported many wildflowers, 

including owl’s clover (Orthocarpus 

purpurascens), lupine (Lupinus spp.), 

brodiaea (Brodiaea spp.) and many others. 

This native grassland community, known 

as valley needlegrass grassland, has been 

almost completely replaced by annual 

grassland. Remnants of valley needlegrass 

grassland occur as small patches, usually 

in marginal habitats, such as undisturbed 

moist sites and areas protected from grazing 

or only lightly grazed. Valley needlegrass 

grassland may occur on the Refuge, 

although no occurrence has been identified. 

Another native perennial grassland that 

was once common is the valley wild rye 

grassland, dominated by creeping wild rye 

and associated with California mugwort 

(Artemisia spp.) and stinging nettle (Urtica 

dioica). Patches of this grassland occur on 

the Refuge and are being actively restored.

Irrigated Pasture. Irrigated pastures on the 

Refuge are irrigated and optimally grazed in 

the summer months (June through August) 

to promote and enhance native vegetation. 

Grazing is monitored to provide a mosaic 

of habitats, thus increasing biodiversity. 

Monitoring consists of visual calibration and 

measuring residual dry matter in pounds 

per acre. These pastures support a good 

ratio of forbs (eg., clovers, lupines, poppies 

and succulent grasses) to grasses, which 

provide valuable forage for white-faced 

ibis (Plegadis chihi), geese, black-bellied 

plovers (Pluvialis squatarola) and others. 

Currently, irrigated pastures, found on 

the North Stone Lakes and Gallagher 

properties, play a valuable role in habitat 

and wildlife management.

Grassland Wildlife. Grassland habitats are 

important foraging areas for many species. 

Less than 1 percent of California’s native 

grassland remains due mainly to advances 

in large-scale irrigation in the 1930s; 

therefore, grassland management plays 

a vital role in contributing to the Refuge 

System’s biological integrity, diversity and 

environmental health. Refuge grassland 

management promotes grasslands at 

varying heights and densities in order to 

create a mosaic of grassland habitats at the 

ecosystem level. Species utilizing grasslands 
Lambert Rd

Franklin Blvd.

South

Stone

Lake

104

Twin Cities Rd

Hood Franklin Rd

North

Stone

Lake

5

Elk Grove Blvd

1/05

Land Cover

Approved Refuge Boundary

Agricultural Croplands

Open Water / Aquatic Bed

Perennial Marsh

Cottonwood Willow Riparian

Developed

Disturbed/Fallow/Bare Land

Grasslands

Irrigated Pasture/ Wet Meadow

Managed Permanent Wetland

Managed Seasonal Wetland

Mixed Riparian

Orchards

Riparian Scrub

Passive Seasonal Wetland

Upland Forest

Valley Oak Riparian

Vernal Pools

Vineyard

1 0.5 0 1 Miles

Stone Lakes

National Wildlife Refuge

Figure 5. Land Cover

1 0.5 0 1 Kilometers

Land Status

Cooperative Agreement

Conservation Easement

Non-Refuge Lands

Owned in Fee Title
38 Stone Lakes NWR Comprehensive Conservation Plan

dominated by shorter grasses include 

birds of prey such as northern harriers 

(Circus cyaneus), white-tailed kites (Elanus 

leucurus), red-shouldered hawks (Buteo 

lineatus) and Swainson’s hawks; shorebirds 

such as the black-bellied plover; wading 

birds such as white-faced ibis, great blue 

herons (Ardea herodias) and great egrets 

(Ardea alba); tree swallows (Tachycineta 

bicolor), cliff swallows (Petrochelidon 

pyrrhonota), barn swallows (Hirundo 

rustica) and other species of birds. Species 

utilizing taller grass habitats include 

savannah and white-crowned sparrows 

(Passerculus sandwichensis, Zonotrichia 

leucophrys) , western meadowlarks 

(Sturnella neglecta), California horned 

larks (Eremophila alpestris), loggerhead 

shrikes (Lanius ludovicianus) as well as 

mammals such as coyote (Canis latrans), 

deer mice (Peromyscus maniculatus), 

pocket gophers (Thomomys bottae), 

black tailed hares (Lepus californicus), 

California voles (Microtus californicus) and 

California ground squirrels (Spermophilus 

beecheyi). Since species often utilize more 

than one habitat type, the aforementioned 

habitats and their associated species are 

generalizations. 

Riparian Forest. Riparian forests 

support the densest and most diverse 

wildlife communities in the Sacramento 

Valley. The diversity of plant species and 

growth forms provide a variety of food and 

microhabitat conditions for wildlife. The 

unique combination of surface water and 

groundwater, fertile soils, high nutrient 

availability and layered vegetation provide 

diverse conditions for wildlife. North and 

South Stone Lakes support riparian scrub 

and forest habitats along with marshes 

dominated by cattail (Typha sp.), tule 

(Schoenoplectus acutus var. occidentalis), 

smartweed (Polygonum sp.) and seasonal 

wetlands. Riparian habitat is also supported 

along some of the ephemeral swales and 

stream courses found in the Refuge.

Riparian areas are particularly important to 

migratory wildlife as they provide corridors 

along migration routes. It is important to 

maintain the integrity and continuity of 

riparian corridors which provide nesting and 

foraging habitat and shelter from inclement 

weather and predation. For these reasons, 

riparian restoration and management is a 

vital part of the Refuge’s habitat and wildlife 

management. Three types of riparian 

forests occur on the Refuge: cottonwood, 

mixed, and valley oak (Quercus lobata). 

Mature riparian forests are diverse, 

multilayered communities associated with 

occasional to frequent flooding and perennial 

subsurface water.

Cottonwood Riparian Forest. Cottonwood 

riparian forests occur along perennial 

streams where inundation occurs every 

spring. The forest canopy is dominated by 

Fremont cottonwood (Populus fremontii) 

and Goodding’s willow (Salix gooddingii) 

typically draped with California grape 

vines (Vitis californica). The understory 

often supports California box elder (Acer 

negundo var. californicum), California 

blackberry (Rubus ursinus), white-stemmed 

raspberry (Rubus leucodermis), buttonbush 

(Cephalanthus occidentalis) and blue 

elderberry (Sambucus mexicana). 

Mixed Riparian Forest. Mixed riparian 

forests occur in areas where the floodwater 

inundation occurs more often and for longer 

periods of time than valley oak and less often 

and for shorter duration than cottonwood. 

Riparian forests 

support the 

densest and most 

diverse wildlife 

communities in the 

Sacramento Valley.

Photo by USFWS
Stone Lakes NWR Comprehensive Conservation Plan 39

Canopy dominants include Fremont 

cottonwood, valley oak, Goodding’s willow, 

red willow (Salix laevigata), yellow willow 

(Salix lucida), California black walnut 

(Juglans hindsii) and California sycamore 

(Platanus racemosa). Common understory 

dominants include California box elder, 

Oregon ash (Fraxinus latifolia), poison 

oak (Toxicodendron diversilobum) and 

buttonbush. California grape envelops trees 

and shrubs in this area, giving this forest a 

jungle-like appearance. 

Valley Oak Riparian Forest. The highest 

portion of the floodplain with the least 

frequent inundation supports the valley oak 

riparian forest. Valley oak riparian forest 

persists in well-drained soils which are not 

extensive within the Refuge boundary. The 

dense forest canopy is dominated by valley 

oak with associated tree species of Oregon 

ash, California sycamore, and California 

black walnut. The understory typically 

supports annual grasses, however, moister 

soils support vines and shrubs, such as 

poison oak, California blackberry and wild 

rose (Rosa californica). 

Valley Oak Woodland. Scattered valley 

oaks form woodland and savanna habitats on 

deep, well-drained alluvial soils. Typically 

the valley oak is the only tree found in this 

community. The understory is usually 

annual grassland, but moister sites support 

shrubs, such as poison oak and wild rose. 

Valley oak woodland is often transitional 

between valley oak riparian forest and valley 

oak savanna. Valley oak woodlands are not 

prominent on the Refuge because of a lack of 

appropriate soils and elevations to support 

their growth; however, valley oak woodland 

can be found on the Beach Lake Unit. 

Wetlands. Two wetland vegetation types 

occur on the Refuge: perennial and seasonal. 

Seasonal vegetation can be divided into 

two categories, vernal pools and seasonal 

vegetation in actively managed wetland 

units or cells. Refuge wetlands are managed 

to maintain and enhance biodiversity, 

particularly for waterbirds, reptiles, 

amphibians and invertebrates. North 

and South Stone Lakes support wetlands 

dominated by cattail, tule and smartweed 

along with seasonal wetlands. The most 

extensive areas of freshwater marsh 

and aquatic bed vegetations in southern 

Sacramento County are at South Stone 

Lake. 

Perennial. Shallow, perennial wetland 

vegetation consists primarily of cattails, 

tules, cottonwood, willow, sedges (Carex

spp.) and rushes (Juncus spp., Scirpus

spp.). The vegetation varies in regards to 

the presence of tules and cattails, both of 

which require more saturated conditions 

than most seasonal wetlands provide. 

Conversely, wetlands also vary in regards to 

watergrass (Echinochloa crus-galli), swamp 

timothy (Crypsis schoenoides) and annual 

smartweed (indicative of seasonal wetlands), 

which require seasonal irrigation, as 

opposed to frequent or constant inundation. 

Seasonal. Seasonal wetland vegetation 

on the Refuge is usually considered 

transitional between perennial wetlands and 

vernal pools. Seasonal wetland vegetation 

consists primarily of watergrass, swamp 

timothy, annual smartweed, curly dock 

(Rumex crispus), cocklebur (Xanthium 

strumarium), sedges and rushes. Seasonal 

wetlands are managed to promote vegetation 

that has relatively higher food value for 

migratory waterbirds, as well as to provide 

The highest portion 

of the floodplain 

with the least 

frequent inundation 

supports valley oak 

dominated riparian 

forest, shown being 

restored above with 

the active support of 

volunteers from the 

Sacramento Tree 

Foundation.

Photo by USFWS
40 Stone Lakes NWR Comprehensive Conservation Plan

cover and substrate 

for birds, mammals, 

reptiles, amphibians 

and invertebrates. 

Vernal Pools. Vernal 

pools are ephemeral 

or seasonal 

shallow pools with 

an underlying 

impervious layer. 

The pools fill with 

rain water in the 

winter and retain 

water through the 

spring until they 

evaporate due to 

the Central Valley’s 

intense summer 

heat. There are 

over 150 plant 

species associated 

with similar vernal 

pool habitat on the nearby Cosumnes River 

Preserve and 90 percent of the plants are 

native with more than half of them being 

endemic. Plants and animals associated 

with vernal pools are adapted to the unique 

environment of vernal pools. For example, 

orcutt grasses (Orcuttia spp.) have a 

submerged vegetative phase with floating 

leaves. As the pools dry, a terrestrial phase 

emerges. Typical vernal pool species include 

downingia (Downingia spp.), Sacramento 

and pilose orcutt grass (Orcuttia 

viscida, Orcuttia pilosa), popcorn flower 

(Plagiobothrys spp.), goldfield (Lasthenia

spp.), vernal pool tadpole shrimp (Lepidurus 

packardi), fairy shrimp (Branchinecta 

lynchi), California tiger salamander 

(Ambystoma californiense), western toad 

(Bufo boreas) and the western spadefoot 

toad (Spea hammondii), although some of 

these species can also be found in some of 

the seasonal wetland units. The majority 

(98 percent) of the Refuge vernal pools can 

be found on the Wetland Preserve Unit, 

with the rest found on the Beach Lake Unit. 

Barely 12 percent of the vernal pools located 

on the Refuge are naturally occurring; 

the remainder have been created over the 

last 14 years as mitigation for vernal pool 

losses due to development. The Wetland 

Preserve Unit is owned in fee title by AKT 

Development Corporation and managed by 

the Refuge under a conservation easement. 

Cattle grazing and prescribed fire are the 

primary management tools for maintaining 

and enhancing vernal pools with grazing 

considered most beneficial for vernal pool 

plants, invertebrates and amphibians 

(J. Marty, TNC, pers. comm.). Primary 

benefits of grazing come from phytomass 

removal and trampling of nonnative invasive 

annual grasses and other weeds in the pool 

margins and surrounding uplands. If left 

unchecked, these non-native plant species 

competitively exclude native vernal pool 

plants, especially around pool margins; 

reduce the inundation period of the pool 

which increases evapotranspiration; 

promote the grow of algae, which appears 

to negatively affect vernal pool crustaceans; 

and can inhibit the overland migration of 

vernal pool-breeding amphibians (Robins 

2002). In addition to discouraging nonnative 

grasses, cattle also compact the soil to where 

grazed vernal pools hold water an average of 

50 days longer than un-grazed vernal pools. 

This enhanced water retention capability 

also provides benefits for plant and wildlife 

species. The Wetland Preserve Unit of the 

Refuge is managed by the Service under 

conservation easement. Refuge staff are 

in the process of developing a grazing 

management plan in cooperation with the 

landowner that will protect vernal pool and 

other seasonal wetland habitats on the unit.

Wildlife

The diverse vegetation of the Beach-Stone 

Lakes Basin provides habitat for a range 

of mammals, birds, reptiles, amphibians 

and invertebrates. Wildlife can be found 

on all units of the Refuge. North and South 

Stone Lakes are especially important 

wildlife habitat areas because of the 

combination of grasslands, extensive 

riparian forest, seasonal and perennial 

wetlands and open water they support. A 

survey of North Stone Lake reported three 

amphibian species, eight reptile species, 

101 bird species and 23 mammal species 

(USFWS 1992). The same survey also 

reported finding active nesting sites of 

The most extensive 

areas of freshwater 

marsh and aquatic 

bed vegetations 

in southern 

Sacramento County 

are at South Stone 

Lake, on the Refuge.

Photo by USFWS
Stone Lakes NWR Comprehensive Conservation Plan 41

52 great egrets, 49 great blue herons, 61 

black-crowned night-herons (Nycticorax 

nycticorax), 20 snowy egrets (Egretta 

thula), and 17 double-crested cormorants 

(Phalacrocorax auritus).

South Stone Lake is rich in riparian and 

wetland habitats supporting a diversity 

of amphibian, reptile, bird and mammal 

species. Two waterfowl hunt clubs were 

operated on the lake for many years prior 

to establishment as a refuge. However, 

hunting success has declined substantially 

during the last three decades. The primary 

waterfowl species likely to be encountered 

at South Stone Lake are mallard (Anas 

platyrhynchos), American wigeon (Anas 

americana), green-winged teal (Anas 

crecca) and occasionally, northern pintail 

(USFWS 1992).

Mammals. Grassland habitats support 

small prey species, such as deer mice, 

California voles, pocket gophers, California 

ground squirrels, desert cottontails 

(Sylvilagus auduboni) and black-tailed 

hares. Ungrazed grasslands with dense 

cover typically support more wildlife 

species than do grazed pastures or 

disturbed grasslands and some species 

prefer ungrazed pastures, such as badgers 

(Taxidea taxus), black-tailed hares, coyotes 

and California ground squirrels.

Valley oak woodlands supply acorns 

for western gray squirrels (Sciurus 

griseus) and black tailed deer (Odocoileus 

hemionus), which depend on the acorns as a 

critical autumn food source. Riparian forest 

and scrub provide habitats for many of the 

same species as the valley oak woodlands. 

Mature cottonwood, Goodding’s willow and 

valley oak trees provide habitat for cavitynesting species, such as bats, western gray 

squirrels, raccoons (Procyon lotor) and 

ringtails (Bassariscus astutus). Riparian 

understory plants, such as California grape, 

blackberry and elderberry, supply food 

sources for Virginia opossum (Didelphis 

virginiana), raccoon, striped skunk 

(Mephitis mephitis) and gray fox (Urocyon 

cinereoargenteus). As with birds, narrow 

and discontinuous riparian areas favor 

wildlife that forage near, in or over water, 

such as beavers (Castor canadensisis), 

river otters (Lutra canadensis) and bats. 

Riparian scrub provides cover and forage 

for California ground squirrels. Beavers 

preferentially feed on young cottonwood 

shoots and many small mammals feed on 

willow seeds. Bramble thickets offer escape 

cover to desert cottontails and black-tailed 

hares. Aquatic areas near riparian scrub 

habitats provide foraging habitats for 

carnivores and omnivores, such as river 

otters and gray foxes. Ground insectivores 

that inhabit riparian scrub include broadfooted moles (Scapanus latimanus). 

Striped skunks also prey on other small 

animals using the riparian scrub.

Perennial wetlands support river otters, 

muskrats (Ondatra zibethicus) and beavers. 

Upland species, such as black-tailed hares 

and desert cottontails, take cover and forage 

at the margins of wetland habitats. 

Birds. Over 200 bird species have been 

sighted at in the Beach-Stone Lakes Basin 

(USFWS 2003a). About 90 species are 

confirmed to have nested on the Refuge. 

These species include numerous waterbirds, 

songbirds, and raptors. For a detailed list of 

birds see Appendix C. 

Refuge grasslands are important foraging 

areas for many birds of prey, such as blackshouldered (white-tailed) kites, red-tailed 

hawks (Buteo jamaicensis), Swainson’s 

hawks, red-shouldered hawks, northern 

harriers, golden eagles (Aquila chrysaetos), 

American kestrels (Falco sparverius), 

prairie falcons (Falco mexicanus), great 

horned owls (Bubo virginianus) and barn 

owls (Tyto alba). Songbirds forage in 

grassland habitats, including loggerhead 

shrikes, yellow-billed magpies (Pica 

nuttalli), horned larks, water pipits 

(Anthus rubescens), western bluebirds 

(Sialia mexicana), savannah sparrows 

and a variety of swallow species. A few 

birds nest in grasslands, such as killdeer 

(Charadrius vociferous), ring-necked 

pheasants (Phasianus colchicus), northern 

harriers, western kingbirds (Tyrannus 

verticalis) and western meadowlarks. 
42 Stone Lakes NWR Comprehensive Conservation Plan

Ungrazed grasslands with dense cover 

typically support more wildlife species 

than do grazed pastures or disturbed 

grasslands. However, some bird species 

prefer grazed pastures, such as burrowing 

owls (Athene cunicularia), mourning doves 

(Zenaida macroura), Brewer’s blackbirds 

(Euphagus cyanocephalus), turkey vultures 

(Cathartes aura), red-tailed hawks, blackshouldered kites, ring-necked pheasants 

and yellow-billed magpies. Pastures on 

the Refuge and nearby farmland may 

represent an important stopover point for 

geese during spring migration; more than 

1,500 white-fronted geese (Anser albifrons) 

were observed on pasture near HoodFranklin Road in the late 1970s (USFWS 

1992) and large numbers continue to use 

grasslands adjacent to North Stone Lake. 

Canada (Branta canadensis), snow (Chen 

caerulescens) and Ross’ (Chen rossii) geese 

are also observed on Refuge pastures 

and waterbodies regularly during spring. 

Except for some species such as robins, 

blackbirds, and mourning doves, vineyards 

provide virtually no suitable bird habitat, 

while orchards can provide some nesting 

habitat for birds of prey and food and cover 

for other birds and mammals.

The mature Fremont cottonwood, willow 

(Salix spp.) and 

valley oak trees of 

riparian vegetation 

provide nesting 

support for large 

birds, such as hawks, 

owls, American 

crows (Corvus 

brachyrhynchos), 

great egrets and 

great blue herons. 

Cavity nesting 

birds, such as 

woodpecker species 

and wood ducks (Aix 

sponsa), require 

mature stands. 

Dense understory 

consisting of 

blackberry (Rubus

spp.), raspberry 

(Rubus spp.), 

California grape and 

elderberry produce 

important food for wildlife. Common 

birds that depend on the nectar, fruits, and 

seeds of riparian plants include California 

towhees (Pipilo crissalis), spotted towhees 

(Pipilo maculatus), Anna’s hummingbirds 

(Calypte anna) and black-headed grosbeaks 

(Pheucticus melanocephalus). 

The high quality riparian vegetation on 

the Refuge provides excellent habitat for 

neotropical migrants. The riparian and 

valley oak woodland vegetation supports 

an abundance of insect prey that sustain 

a high diversity and density of migratory 

and resident birds, including western 

flycatchers (Empidonax difficilis), 

yellow warblers (Dendroica petechia), 

MacGillivray’s warblers (Oporornis tolmiei) 

and song sparrows (Melospiza melodia). 

Habitat destruction and nest parasitism 

by nonnative brown-headed cowbirds 

(Molothrus ater) may be primary causes of 

bird decline on the Refuge (USFWS 1992). 

Insectivorous species that have dramatically 

declined or been eliminated from the Central 

Valley’s nesting avifauna, but have been 

seen on the Refuge, include: yellow-billed 

cuckoos (Coccyzus americanus), willow 

flycatchers (Empidonax spp.), yellow 

Pastures on 

the Refuge and 

nearby farmland 

may represent an 

important stopover 

point for geese 

during spring 

migration; Canada, 

snow, white-fronted, 

and Ross’ geese are 

regularly observed 

on Refuge pastures 

and waterbodies 

during spring.

Photo by USFWS
Stone Lakes NWR Comprehensive Conservation Plan 43

warblers, yellow-breasted chats (Icteria 

virens) and blue grosbeaks (Passerina 

caerulea). Some riparian areas are narrow 

and discontinuous and favor wildlife 

species that forage in adjacent grassland 

or agricultural fields, including blackshouldered kites, American kestrels and 

western kingbirds. Riparian areas also 

provide perches and cover for species that 

forage in or over water, such as doublecrested cormorants, green-backed herons 

(Butorides virescens), belted kingfishers 

(Ceryle alcyon), black phoebes (Sayornis 

nigricans) and violet-green swallows 

(Tachycineta thalassina). Riparian scrub 

provides cover and forage for California 

(valley) quail (Callipepla californica), ringnecked pheasants, American goldfinches 

(Carduelis tristis), lesser goldfinches 

(Carduelis psaltria) and California towhees. 

Bramble thickets provide potential nesting 

habitat for tri-colored blackbirds (Agelaius 

tricolor). Aquatic areas near riparian 

scrub habitats provide foraging habitats 

for ground insectivores, such as killdeer, 

spotted sandpipers (Actitis macularius) and 

western kingbirds. 

Valley oak woodlands provide shade, shelter 

and nesting habitat for many bird species, 

including various woodpecker species and 

other cavity-nesting birds, such as American 

kestrels, western screech owls (Megascops 

kennicottii), white-breasted nuthatches 

(Sitta carolinensis) and western bluebirds. 

Acorns are an important food source for 

many species, including acorn woodpeckers 

(Melanerpes formicivorus), valley quail, 

northern flickers (Colaptes auratus) and 

scrub jays (Aphelocoma californica). 

Valley oak foliage and bark attract insects 

that are eaten by ash-throated flycatchers 

(Myiarchus cinerascens), plain titmice 

(Baeolophus inornatus), white-breasted 

nuthatches and northern orioles (Icterus 

galbula). Valley oak woodlands provide 

the best habitat on the Refuge for aerialforaging species, such as acorn woodpeckers, 

ash-throated flycatchers and western 

wood-pewees (Contopus sordidulus). This 

habitat also offers perch sites for ground 

foraging species, such as western bluebirds 

and northern flickers. Swainson’s hawks, 

red-tailed hawks and black-shouldered kites 

use valley oak woodlands as habitat because 

they require sturdy nesting sites with 

open canopy for easy access. Great blue 

heron and great egret maintain important 

rookeries in the valley oak woodlands near 

North Stone Lake and near Black Crown 

Lake on the Bufferlands Unit.

Perennial wetlands provide habitat for a 

variety of species, including pied-billed 

grebe (Podilymbus podiceps), American 

bitterns (Botaurus lentiginosus), American 

coots (Fulica Americana) and Virginia rails 

(Rallus limicola). Upland species, such 

as ring-necked pheasants and California 

quail, take cover and forage at the margins 

of wetland habitats. Diving and dabbling 

ducks and other aquatic birds also use the 

perennial wetlands of North and South 

Stone Lakes and the Bufferlands; however, 

most wintering waterbirds depend on the 

seasonal wetlands.

Waterbirds that make extensive use of 

the managed wetlands at North Stone 

Lake and the Bufferlands include grebes, 

herons, egrets, pelicans, cormorants, rails, 

cranes, plovers and other waterbird species 

(USFWS 1992). Flooded pastures and 

croplands and other seasonal wetlands 

provide foraging and roosting habitat 

for thousands of shorebirds migrating 

along the Pacific Flyway. For example, 

4,090 shorebirds and 4,440 waterbirds 

were observed at Upper Beach Lake in a 

single survey on April 28, 1990 (USFWS 

1992). A DFG aerial survey conducted in 

February 1972 recorded 5,750 waterfowl 

in the Beach-Stone Lakes basin. As many 

as 15,000 waterfowl were observed on 

other surveys (USFWS 1992). Dominant 

waterfowl species included tundra swans 

(Cygnus columbianus), snow geese, whitefronted geese, Canada geese, mallards, 

northern pintails, northern shovelers (Anas 

clypeata), cinnamon teal (Anas cyanoptera), 

green-winged teal, wood ducks and ruddy 

ducks (Oxyura jamaicensis). The Service 

also collected data on waterbird abundance 

in the Beach-Stone Lakes basin during 

January through March in 1982 and 1983. 

The basin supported two million annual 
44 Stone Lakes NWR Comprehensive Conservation Plan

bird use days (one bird present for one 

day); of these 1.2 million were waterfowl 

(USFWS 1992). Based on the observations 

of local landowners and data collected by 

the Service, DFG and Ducks Unlimited, the 

Refuge appears to be most important as a 

feeding and resting area for waterfowl in 

the early spring rather than an important 

overwintering area. North and South Stone 

Lakes have the potential to be managed 

as waterfowl breeding and nesting areas 

during the spring and summer (USFWS 

1992). Other wetland obligate bird species 

include common yellowthroats (Geothlypis 

trichas), red-winged blackbirds (Agelaius 

phoeniceus) and marsh wrens (Cistothorus 

palustris). 

Open water portions of the Refuge’s lakes, 

ponds and sloughs offer roosting habitat 

for waterbirds, such as pied-billed grebes, 

eared grebes (Podiceps nigricollis), common 

moorhens (Gallinula chloropus), American 

coots and a variety of waterfowl species. 

Diving and dabbling ducks and other water 

birds forage on submerged aquatic plants 

and associated invertebrates in aquatic beds 

associated with open water. Fisheries in 

open waters of Beach Lake, and North and 

South Stone Lakes provide an important 

food source for fish eating species, including 

American white pelicans (Pelecanus 

erythrorhynchos) and double-crested 

cormorants. In addition, double-crested 

cormorants nest at North Stone Lake 

(USFWS 1992).

Reptiles and Amphibians. Reptiles and 

amphibians can be found among the various 

habitat types on the Refuge. Common 

reptiles and amphibians on the Refuge 

include Pacific treefrogs (Hyla regilla), 

bullfrogs (Rana catesbeiana), western 

pond turtles (Clemmys marmorata), 

pond slider turtles (Trachemys scripta), 

western fence lizards (Sceloporus 

occidentalis), western terrestrial garter 

snakes (Thamnophis elegans elegans) 

and gopher snakes (Pituophis catenifer). 

Suitable habitat exists for the federallythreatened giant garter snake along 

sparsely vegetated lakes, sloughs and 

wetlands. Refuge grassland habitats 

commonly support gopher snakes, common 

garter snakes (Thamnophis sirtalis), 

California kingsnakes (Lampropeltis 

getulus californiae), western fence lizards 

and western toads. Valley oak woodland 

reptiles observed at North Stone Lake 

include western fence lizards, California 

alligator lizards (Elgaria multicarinata 

multicarinata), western yellow-bellied 

racers (Coluber mormon), Pacific gopher 

snakes, California kingsnakes and common 

garter snakes. Amphibians have also been 

seen in the valley oak woodlands at North 

Stone Lake, including bullfrogs, western 

toads and Pacific treefrogs. Reptiles seen 

in the riparian scrub include the ground 

insectivorous western fence lizard and the 

predatory gopher snake. Perennial wetland 

habitat provides breeding and foraging 

habitat for common garter snakes, Pacific 

treefrogs and bullfrogs. This habitat also 

has the potential to provide habitat for the 

giant garter snake. When standing water 

is available, amphibians such as California 

tiger salamanders, western toads and Pacific 

treefrogs use vernal pools for egg laying and 

Refuge grassland 

habitats commonly 

support reptiles like 

this rehabilitated 

gopher snake, shown 

being released onto 

the Refuge.

Photo by USFWS
Stone Lakes NWR Comprehensive Conservation Plan 45

for the development of their young.

Fish. Fish are found in all bodies of water 

on the Refuge, including North and South 

Stone Lakes. Various surveys done from 

1992 to present have yielded 30 species on 

the Refuge (See Appendix D, Fish Species 

Found on Stone Lakes NWR). Only 

five of the species observed, Sacramento 

blackfish (Orthodon microlepidotus), prickly 

sculpin (Cottus asper), hardhead minnow 

(Mylopharodon conocephalus), California 

roach (Hesperoleucus symmetricus) and 

sculpin are California natives. Common 

fish on the Refuge include mosquito fish, 

threadfin shad (Dorosoma petenense), black 

crappie (Pomoxis nigromaculatus), redear 

sunfish (Lepomis microlophus), catfish 

(Ictalurus spp.), largemouth bass, carp 

(Cyprinus carpio) and common bluegill 

(Lepomis macrochirus) (D. Vanicek , CSUS, 

1999, B. Treiterer, USFWS, pers. comm.). 

Other introduced species include silverside 

(Menidia beryllina) and shrimp species. 

While many problems are associated with 

introduced fishes, they have a value for 

sportfishing (largemouth bass, catfish, etc.), 

controlling mosquitoes (Gambusia spp.), and 

as forage for other fish and wildlife. 

North and South Stone Lakes are best 

described as shallow and eutrophic, 

characterized by enriched dissolved nutrient 

levels (such as phosphates) that stimulate 

growth of aquatic plants and algae. As 

the abundant plants and algae decay the 

dissolved oxygen levels are reduced by 

microbial blooms. Due to the abundant 

plankton, these lakes are dominated by 

planktivorous (plankton-eating) fish. The 

food chain is stimulated by nutrients from 

abundant bird use, which helps produce 

the dense phytoplankton population. The 

phytoplankton in turn support a large 

zooplankton population, which supports the 

fish. Piscivorous (fish-eating) fish are not 

abundant in the lakes. The SP cut is less 

turbid than the lakes and contains fewer 

planktivorous fish. 

Aquatic habitats occurring on the 

Bufferlands of the SRWTP consist of 

Laguna and Morrison creeks and five 

lakes. A total of 22 fish species have been 

documented from Bufferlands waterbodies. 

Meadowlark Lake comprises 19 acres of 

permanent water and was created as a 

borrow pit for construction of Interstate5. It is filled each winter from overflows of 

Morrison and Laguna creeks and has steep 

banks with almost no vegetation. Black 

Crown Lake covers 28 acres and is very 

similar in nature and origin to Meadowlark 

Lake. However, it has some vegetation for 

cover and shade, is connected to Morrison 

Creek, and has a more stable water level 

in summer. Nineteen and 21 species of fish 

have been documented from Meadowlark 

and Black Crown lakes, respectively. 

Nicolaus Pond is an 8 acre pond, fed with 

water from a leased aquaculture facility on 

the Bufferlands. The banks are gradual 

and contain some grassy areas and some 

emergent vegetation. Five species of fish 

have been found in this pond. Fishhead 

Lake was created as part of a wetland 

mitigation project. The lake consists of 13.5 

acres of permanent water with an additional 

30.5 acres of seasonal water. Tailwater from 

Laguna Creek Fish Farm feeds the lake 

almost year round. The banks are steep, but 

stable water levels have allowed emergent 

vegetation to become established. The lake 

contains 18 species of fish. The 6.2-acre Lost 

Lake was formed from an abandoned gravel 

mining operation. Most of the lake is about 

ten feet deep and steep sided. Five species 

have been found in Lost Lake.

About 16,000 lineal feet of Laguna Creek 

passes through the Bufferlands. It is not 

channelized and appears to be high quality 

fish habitat. The upper sections have 

gentle slopes and large patches of emergent 

vegetation while the lower sections are lined 

with mature riparian trees. A total of 14 

species of fish have been found in the creek. 

A 15,000 lineal foot section of Morrison 

Creek runs through the Bufferlands and 

receives most of its summer water from 

Sacramento storm drains. Fish kills have 

been observed here in the past, possibly 

a consequence of impaired water quality. 

Above its confluence with Laguna Creek, 

Morrison Creek is highly channelized 

and appears to have little high quality 
46 Stone Lakes NWR Comprehensive Conservation Plan

fish habitat. Some stretches of bank are 

vegetated; however, most banks are steep 

and bare when water levels recede during 

the summer. In summer, large patches 

of floating water primrose (Ludwigia 

peploides) sometimes cover the entire 

surface of the creek. Past the confluence, 

the banks are lined with riparian trees 

offering a higher degree of cover. Ten 

species of fish have been found in Morrison 

Creek.

Invertebrates. There has been no 

comprehensive invertebrate survey 

conducted at the Refuge. However, 

some surveys occasionally conducted by 

SYVCMD and refuge staff have found that 

aquatic vertebrates, such as grass shrimp, 

Louisiana swamp crayfish, clam shrimp 

(Cyzicus californicus), Odonata larvae 

(dragon and damselfly), Notonectiday larvae 

(backswimmers), cladocerans, copepods and 

water beetles (Corixidae larvae), inhabit 

seasonal and permanent wetlands and also 

the vernal pools. 

Vernal pools are located on the Wetland 

Preserve, North Stone Lake and Beach 

Lake units of the Refuge. Please see the 

description of vernal pool fairy shrimp and 

vernal pool tadpole shrimp below. Two 

species of fairy shrimp, the vernal pool fairy 

shrimp and the vernal pool tadpole shrimp, 

have been identified in the pools.

Special Status Species 

Stone Lakes provides or has the potential 

to provide habitat for Federal Endangered 

Species Act (ESA) and California 

Endangered Species Act (CESA) threatened 

and endangered species.

Federally-listed Species

Vernal pool fairy shrimp (Branchinecta 

lynchi). The vernal pool fairy shrimp is 

an ESA listed threatened species and is a 

small (0.4 inches to 1.0 inch long) crustacean 

with a delicate elongate body, large stalked 

compound eyes and 11 pairs of swimming 

legs. This species is endemic to vernal pool 

habitats in California and southwestern 

Oregon (USFWS 1994).

Vernal pool fairy shrimp typically inhabit 

vernal pools with clear to tea-colored water, 

most commonly in grass or mud-bottomed 

swales, or basalt flow depression pools 

in unplowed grasslands. They also may 

exist in alkaline vernal pools. The water 

in pools inhabited by this species has low 

total dissolved solids, low conductivity, low 

alkalinity and low chloride. Fairy shrimp 

feed on algae, bacteria, protozoa, rotifers 

and bits of detritus (USFWS 1994). 

The primary threats to vernal pool fairy 

shrimp are the loss and alteration of habitat 

due to urban and agricultural development 

and random extinction by virtue of the small 

isolated nature of the remaining population. 

Vernal pools are found on the Wetland 

Preserve and Beach Lake units. Vernal pool 

fairy shrimp have been documented within 

vernal pools on the Wetland Preserve Unit.

Vernal pool tadpole shrimp (Lepidurus 

packardi). The vernal pool tadpole shrimp 

is an ESA listed endangered species. Vernal 

pool tadpole shrimp are primarily benthic 

(living on the bottoms of the pools) animals 

that swim with their legs down. Vernal 

pool tadpole shrimp climb or scramble over 

objects, and plow along bottom sediments 

as they forage for food. Their diet consists 

of organic detritus and living organisms, 

such as fairy shrimp and other invertebrates 

(USFWS 2003c). Females disperse fully 

developed cysts into the pool, where the 

cysts are then deposited into the sediment. 

Vernal pool tadpole shrimp pass the summer 

months as dormant cysts in the soil. Some of 

the cysts hatch as the vernal pools are filled 

with rainwater in the next or subsequent 

seasons, while other cysts may remain 

dormant in the soil for many years. When 

winter rains refill inhabited pools, tadpole 

shrimp reestablish from dormant cysts and 

can become sexually mature within three 

to four weeks of hatching (Ahl 1991; Helm 

1998). The tadpole shrimp will continue to 

grow as long as their vernal pool habitat 

remains inundated, in some cases for six 

months or longer. They periodically shed 

their shells, which can often be found along 

the edges of vernal pools where vernal pool 

tadpole shrimp occur. Mature vernal pool 
Stone Lakes NWR Comprehensive Conservation Plan 47

tadpole shrimp range from 0.6 to 3.4 inches 

in length. Mature adults may be present in 

pools until the habitats dry up in the spring 

(USFWS 2003c).

Tadpole shrimp can be found in California’s 

Central Valley and the San Francisco Bay 

area. The geographic range of this species 

includes disjunct occurrences in the Central 

Valley, from Shasta County to northern 

Tulare County and in the Central Coast 

Range from Solano County to Alameda 

County. The primary threats to vernal 

pool tadpole shrimp are the same as for the 

vernal pool fairy shrimp. 

Vernal pools can be found on the Wetland 

Preserve and Beach Lake units. Vernal 

pool tadpole shrimp have been documented 

within vernal pools on the Wetland Preserve 

Unit.

Valley elderberry longhorn beetle 

(Desmocerus californicus dimorphus, 

VELB). The valley elderberry longhorn 

beetle is an ESA listed threatened species. 

The VELB is a medium-sized beetle, 

typically about two cm long. 

The VELB is associated with elderberry 

trees (Sambucus spp.) during its entire life 

cycle. The adults emerge from pupation 

inside the wood of these trees in the spring 

as their flowers begin to open. The exit 

holes made by the emerging adults are 

distinctive small oval openings. Often these 

holes are the only detectable clue that the 

beetles occur in an area. The adults feed on 

elderberry foliage until about June, when 

they mate. The females lay eggs in crevices 

in the bark. Upon hatching, the larvae begin 

to tunnel into the tree where they will spend 

one to two years eating the interior wood, 

which is their sole food source.

The elderberry tree is associated with 

riparian forests which occur along rivers 

and streams. Historically the VELB 

ranged throughout the Central Valley; 

however, recent surveys have revealed the 

VELB to persist only in scattered localities 

along the Sacramento, American, San 

Joaquin, Kings, Kaweah and Tule rivers 

and their tributaries. Over 95 percent of 

our riparian forests have been cleared in 

the past century for agricultural, as well 

as urban and suburban, and development 

uses (Smithsonian Zoological Park). The 

wood from these forests has also been used 

extensively as fuel and building materials. 

Additionally, extensive use of pesticides, 

grazing and other mismanagement have 

severely degraded otherwise undisturbed 

patches of riparian habitat.

There are no documented sightings of the 

VELB or of any exit holes on the Refuge. 

However, elderberry trees of appropriate 

size can be found on the Beach Lake 

Unit. New elderberry shrubs planted for 

mitigation on the South Stone Lake Unit are 

expected to reach the appropriate size for 

VELB habitat in the future.

Giant garter snake (Thamnophis gigas). 

The giant garter snake is an ESA listed 

threatened species. Historically, the range 

of this snake was the San Joaquin Valley 

from the vicinity of Sacramento and Antioch 

southward to Buena Vista and the Tulare 

Lake Basin (CDFG 2000). The current 

distribution extends from near Chico to 

Fresno County. This species is one of the 

most aquatic garter snakes and is usually 

found in areas of freshwater marsh and low 

gradient streams. Permanent wetlands 

are especially important as they provide 

habitat over the summer and early fall when 

seasonal wetlands are dry. Although the 

snake is absent from larger rivers (such 

as the Sacramento River), it has adapted 

to human made habitats, such as drainage 

canals and irrigation ditches, especially 

those associated with rice farming. Riparian 

woodlands do not provide suitable habitat 

because of excessive shade and inadequate 

prey resources (USFWS 1993). 

Generally quite aquatic, these garter snakes 

forage primarily in and along streams, 

taking fish, amphibians and amphibian 

larvae (Fitch 1941). Most current food 

sources may be introduced species, such as 

carp, mosquito fish, and bullfrogs, because 

the native prey such as blackfish, thick-tailed 

chub (Gila crassicauda) and red-legged 
48 Stone Lakes NWR Comprehensive Conservation Plan

frog (Rana aurora draytoni) are no longer 

available (Rossman et al. 1996). Courtship 

and mating normally occur soon after spring 

emergence. Young are born alive between 

mid-July and early September, usually in 

secluded sites, such as under the loose bark 

of rotting logs or in dense vegetation near 

pond or stream margins. 

The giant garter snake is now very scarce 

throughout its range in the Central Valley. 

Populations have been eliminated or 

decimated by the elimination of natural 

sloughs and marshy areas. Heavy use of 

pesticides is also suspected as a contributing 

factor in the decline of this once abundant 

garter snake. Fortunately, protection of 

waterfowl habitat may allow it to survive in a 

small portion of its original range. 

The giant garter snake was last documented 

on the Refuge 14 years ago in 1992 at Beach 

Lake. The species is presumed to be present 

throughout the Refuge where suitable 

habitat exists (Wylie 1997). The Refuge lies 

within the Sacramento Basin subpopulation 

of the giant garter snake.

Bald eagle (Haliaeetus leucocephalus). 

The bald eagle has suffered from habitat 

destruction and degradation, illegal shooting 

and contamination of its food source, most 

notably due to the pesticide DDT. The 

bald eagle is listed as an ESA threatened 

and CESA endangered species. Although 

there have been no documented sightings 

of the bald eagle on the Refuge, (DFG 2004) 

habitat exists for them on the Refuge.

State-Listed Species

Greater sandhill crane. The greater sandhill 

crane is a CESA listed threatened species. 

The Refuge and adjacent public and private 

lands provide habitat for greater and lesser 

sandhill (Grus canadensis canadensis) 

cranes. The California Central Valley 

provides wintering habitat for 6,000 – 6,800 

cranes, nearly 14 percent of the world’s 

total population of greater sandhill cranes 

(Pacific Flyway Council 1997). The San 

Joaquin-Sacramento Delta is one of the two 

most important winter use areas for the 

Central Valley population of greater sandhill 

cranes; over 61 percent of the Central Valley 

population has been recorded on the Delta 

(Ivey and Herziger 2001).

Historically, greater sandhill cranes were 

fairly common breeders on California’s 

northeastern plateau (Grinnell and Miller 

1944). The greater sandhill crane is now 

reduced greatly in numbers and breeds 

only in Siskiyou, Modoc, Lassen, Plumas 

and Sierra counties (James 1977; Remsen 

1978; McCaskie et al. 1979). The subspecies 

winters primarily in the Sacramento and 

San Joaquin Valleys (Grinnell and Miller 

1944) but can also be found near Brawley in 

Imperial County and Blythe, in Riverside 

County (Garrett and Dunn 1981), along with 

lesser sandhill cranes. Greater sandhill 

cranes formerly wintered more commonly 

in Southern California, but have declined 

greatly there and throughout their range. 

They are extremely rare outside of their 

known wintering grounds except while 

migrating over interior California. There 

have been a few coastal sightings from 

Marin County southward, but there are no 

records from offshore islands.

The Refuge’s wintering cranes migrate 

southward from the northeast in September 

and October and northward in March and 

April. Cranes travel in great flocks, both 

day and night, with stops only for short 

periods to feed and rest. Migration is rapid 

and direct. In winter, cranes frequent dry 

grasslands and croplands especially near 

open and emergent wetlands (Grinnell 

and Miller 1944), although they may also 

feeds on dry plains far from water. When 

foraging, cranes prefer open treeless short 

grass plains, grain fields and open wetlands 

where predators can be easily seen (Grinnell 

and Miller 1944, Cogswell 1977). They feed 

mostly on cereal crops (e.g., newly planted 

or harvested) and will also consume grasses 

and forbs. Cranes also use their long bills to 

probe in soil for roots, tubers, seeds, grains, 

earthworms and insects. Larger prey, such 

as mice, small birds, snakes, frogs, and 

crayfish, are also taken (Terres 1980; Eckert 

and Karalus 1981). Fruits and berries are 

eaten if available (Eckert and Karalus 1981). 

Grazing can be detrimental to sandhill 
Stone Lakes NWR Comprehensive Conservation Plan 49

crane, when they are nesting and fledging 

(Littlefield and Ivey 2002), however nesting 

is not known to occur on the Refuge. 

Cranes roost at night in flocks standing 

in moist fields or in shallow water (Terres 

1980). They also roost in expansive, dry 

grasslands, island sites, and wide sandbars 

(Johnsgard 1975; Eckert and Karalus 1981).

In California, sandhill cranes establish 

nesting territories in wet meadows that are 

often interspersed with emergent marsh 

habitat. The last statewide breeding 

population study in California was conducted 

in 1988. The breeding population in 

California was estimated to be 276 pairs. 

Favorable roost sites and an abundance 

of cereal grain crops characterize the 

cranes’ preferred Central Valley wintering 

ground. Rice is used extensively by cranes 

near the Butte Sink area of Butte County 

and corn is the principal food source at 

most other Central Valley wintering areas, 

particularly in the Sacramento-San Joaquin 

Delta near Lodi in San Joaquin County. 

Irrigated pastures are chosen for resting 

sites throughout the wintering ground. A 

key requirement of wintering habitat is a 

communal roost site consisting of an open 

expanse of shallow water (CDFG 2000). 

Currently, the estimate for greater sandhill 

cranes within their Pacific Flyway range is 

between 5,000 and 6,000 individuals. This 

species continues to experience threats on 

both wintering and breeding grounds by 

agricultural and residential conversion of 

habitat, predation, human disturbance and 

collisions with power lines (CDFG 2000).

Surveys indicate 300-350 greater sandhill 

cranes feed, roost and loaf on the Refuge 

during the winter season. The cranes roost 

and forage in managed impoundments, 

pastureland, and other agricultural land 

throughout and adjacent to the Refuge. 

Cranes are commonly seen on irrigated 

pastures on the South Stone Lake Unit and 

on the grasslands of North Stone Lake and 

the Wetland Preserve Unit. They can also 

be found on the Whitney (in the southeast 

corner) and Zacharias Island properties, 

lands that are not managed by the Refuge 

but are within the approved refuge 

boundary. In general, a mix of greater and 

lesser sandhill cranes can be found south 

of Hood-Franklin Road, with only greater 

sandhill cranes occurring north of HoodFranklin Road. 

Swainson’s hawk (Buteo swainsoni). 

The Swainson’s hawk is a State-listed 

threatened species. The Swainson’s hawk 

is an uncommon breeding resident in the 

Central Valley (Polite 2000). Swainson’s 

hawks breeding in the Central Valley appear 

to winter in Mexico and Columbia (CDFG 

2001). Bloom (1980) estimated 110 nesting 

pairs, and a total of 375 pairs in California 

(Polite 2000). The diet of the Swainson’s 

hawk is varied, although its staple in 

the Central Valley is the California vole, 

augmented with a variety of bird and insect 

species. Over 85 percent of Swainson’s 

hawk territories in the Central Valley are 

in riparian systems adjacent to suitable 

foraging habitats. Swainson’s hawks often 

nest peripherally to riparian systems of 

the valley, as well as within lone trees or 

groves of trees in agricultural fields. Valley 

oak, Fremont cottonwood, walnut and large 

willow are the most commonly used nest 

trees in the Central Valley, each with an 

average mature height of about 58 feet, 

When foraging, 

greater sandhill 

cranes prefer open 

treeless short grass 

plains, grain fields 

and open wetlands 

where predators can 

be easily seen.

Photo by USFWS
50 Stone Lakes NWR Comprehensive Conservation Plan

and ranging from 

41 to 82 feet tall. 

Swainson’s hawks 

require large, open 

grasslands with 

abundant prey in 

association with 

suitable nest trees. 

Suitable foraging 

areas include 

native grasslands 

or lightly grazed 

pastures, alfalfa 

and other hay crops 

and certain grain 

and row croplands. 

Unsuitable foraging 

habitat includes 

crops, such as 

vineyards, orchards, 

certain row crops, 

rice, corn and cotton 

crops. Suitable 

nest sites may be found in mature riparian 

forests, lone trees or groves of oaks, other 

trees in agricultural fields and mature 

roadside trees.

Declining numbers of Swainson’s hawks 

are, in part, caused by loss of nesting 

habitat (Polite 2000). Converting 

compatible agricultural lands to residential 

and commercial developments and 

noncompatible agricultural activities are 

a serious threat to Swainson’s hawks 

throughout California (CDFG 2000). 

Swainson’s hawks have been seen on nearly 

the entire Refuge (B. Treiterer, USFWS, 

pers. comm.).

Other species that have been seen on the 

Refuge include the following State or 

Federal species of concern: white-faced ibis, 

tri-colored blackbird, western burrowing 

owl, oak titmouse (Baeolophus inornatus), 

white-tailed kite, loggerhead shrike, rufous 

hummingbird (Selasphorus rufus), lamprey 

(Lampetra ayresii), Pacific lamprey, smallfooted bat (Myotis ciliolabrum) and Yuma 

myotis bat (Myotis yumanensis).

Visitor Services 

Ecoregion Scale

Wildlife viewing is the most popular 

wildlife-dependent activity among 

ecoregion residents with 56 percent of 

outdoor recreationists participating. About 

41 percent of residents participate in 

freshwater fishing, 19 percent in saltwater 

fishing and 9 percent in hunting. 

The population in the ecoregion is expected 

to rise by 47 percent between the year 2000 

and the year 2020. Unmet demand appears 

to be highest in the region for wildlife 

viewing, trail hiking, picnicking, camping 

and freshwater fishing with this trend 

expected to continue. Outdoor recreationists 

in the Central Valley/San Francisco Bay 

Ecoregion tend to be mostly white (78 

percent) with growing participation by the 

Hispanic and Asian-American communities. 

In general, residents of moderate or high 

family incomes have the greatest interest 

in wildlife-dependent recreation, both 

consumptive and non-consumptive types. 

The nearest other national wildlife refuges 

are Antioch Dunes, San Pablo Bay, Sutter 

and San Joaquin River. Of these, only Sutter 

is open to unsupervised visitor use. Other 

Many species of 

concern have been 

seen on the Refuge 

including this 

tricolored blackbird.

Photo by USFWS

Wildlife viewing is the most popular wildlife-dependent activity 

among ecoregion residents with 56 percent of outdoor recreators 

participating.
Stone Lakes NWR Comprehensive Conservation Plan 51

nearby public lands offering similar wildlifedependent recreational activities include the 

Yolo Basin Wildlife Area, Cosumnes River 

Preserve and the American River Parkway. 

The U.S. Forest Service and Bureau of 

Land Management have considerable land 

holdings in the ecoregion and all wildlifedependent priority recreational uses are 

accommodated on various portions of their 

lands. There are 16 State Wildlife Areas or 

Ecological Areas operated by DFG within 

an hour’s drive of the Refuge. These 16 

areas provide opportunities for wildlife 

observation, interpretation, hunting and/or 

fishing. In addition, there are five State 

Parks within approximately one hour’s drive 

that offer fishing, wildlife observation and/or 

interpretation. 

Local Scale 

More than 50 percent of lands within the 

Refuge’s approved boundary are privatelyowned and the Service has no authority 

to provide for visitor use of those lands. 

However, limited visitor use is available 

on Refuge lands that are owned by or 

over which the Service has management 

authority. 

Wildlife-Dependent Recreation.

In the Refuge System Improvement 

Act of 1997, Congress recognized six 

wildlife-dependent priority recreational 

uses of refuges: hunting, fishing, wildlife 

observation and photography, interpretation 

and environmental education. More than 

6,000 people per year visit the Refuge to 

participate in a variety of wildlife dependent 

recreational and educational activities. 

Currently, the Refuge accommodates 

waterfowl hunting, wildlife observation 

and photography, interpretation and 

environmental education.

Hunting. In 2004, the Service began a 

planning process for a public waterfowl hunt 

program on the South Stone Lake Unit of 

the Refuge. The first Refuge-managed hunt 

occurred during the 2005-2006 hunt season. 

The program consists of spaced-blinds 

accessible by foot and boat and emphasizes 

opportunities for youth and hunters in 

wheelchairs. Prior to acquisition by the 

Service, waterfowl hunting had occurred 

on the South Stone Lake Unit on the Sun 

River and Lodi Gun Club properties while 

they were private duck hunting clubs. 

Some illegal waterfowl hunting also occurs 

occasionally in the Beach Lake, North Stone 

Lake, and South Stone Lake units due 

to limitations in Refuge law enforcement 

capability and opportunities to gain illegal 

access via private property and by boat.

Wildlife Observation and Photography. The 

Refuge, with its proximal location to a major 

urban center, wildlife diversity and mosaic of 

habitats, is steadily increasing in popularity 

with the surrounding community. The 

North Stone and Beach Lake units of the 

Refuge are open every second and fourth 

Saturday of each month (except during July 

and August) from 7:30 a.m. to 2:00 p.m. and 

9:00 a.m. to 3:00 p.m., respectively. Visitors 

access the Refuge from the trailhead at 

the Elk Grove Boulevard entrance, west of 

Interstate-5. Refuge staff and/or volunteers 

greet visitors who may take a 3-mile round 

trip self-guided walk through grasslands on 

the North Stone Lake unit, past seasonal 

and permanent wetlands, and along 

riparian habitat to an observation platform 

overlooking Lower Beach Lake and wetland 

impoundments. Visitors in wheelchairs or 

with small children may drive directly to the 

universally accessible trail leading to the 

viewing platform. Visitors typically spend 

The first Refugemanaged hunt 

occurred in the 

2005/2006 hunt 

season, including 

this wheelchair 

accessible hunting 

blind on the South 

Stone Lake Unit.

Photo by USFWS
52 Stone Lakes NWR Comprehensive Conservation Plan

between two and four hours per visit and 

there is no daily entrance fee.

Environmental Education. Since the 

establishment of the Refuge, educators and 

youth care professionals from Sacramento, 

San Joaquin and Yolo counties have been 

using the Refuge as an outdoor classroom 

to enhance course curricula. Educators 

include teachers, professors and outdoor 

education leaders. Youth care 

professionals include leaders for 

Scouts, 4H, Campfire and church 

groups. Most of the educators 

and youth care professionals 

who are served by the Refuge’s 

environmental education program 

work with kindergarten through 

college age students. Currently, 

most educational field trips are 

guided by Refuge volunteers or 

staff on the Beach Lake Unit, with 

occasional classroom visits. These 

programs are available by special 

arrangement. 

Interpretation. Current 

Refuge interpretation consists 

of interpretative panels on the 

wildlife viewing platform, Refuge 

brochures, special guided tours 

by Refuge volunteers and staff, 

Refuge website and special events 

such as the Refuge’s annual Walk 

on the Wildside event. 

Fishing. The Refuge does not currently 

have a formal fishing program open to the 

public, although several points of illegal 

entry exist and are regularly used by shore 

and boat anglers.

Non-Priority Visitor Uses Before 

its establishment as a national wildlife 

refuge, a number of visitor uses occurred 

on the Refuge. The EIS (USFWS 1992) 

described recreational resources and uses 

that were cited in “...public comments on 

the draft EIS, staff of land management 

organizations and agencies in the study 

area, representatives of recreation and 

conservation groups, marina operators, 

Sacramento County Sheriff ’s Department 

boat patrol members and boaters who 

regularly recreate on the waterways in the 

study area.” Many of these historic uses 

continue in addition a number of other 

authorized and unauthorized non-priority 

wildlife dependent visitor uses occur on the 

Refuge including: bird-watching and nature 

study (e.g., National Audubon Society 

annual “Christmas bird counts”); target 

shooting/firearm discharging; hunting 

Refuge visitors may take a 3-mile round trip, selfguided walk through managed grasslands and along a 

riparian zone to an observation platform overlooking a 

managed wetland.

Photo by USFWS

Since the 

establishment of the 

Refuge, educators 

and youth care 

professionals 

from Sacramento, 

San Joaquin and 

Yolo counties 

have been using 

the Refuge as an 

outdoor classroom 

to enhance course 

curricula.

Photo by USFWS
Stone Lakes NWR Comprehensive Conservation Plan 53

(mostly pheasant and waterfowl); trapping 

(to control populations of burrowing animals, 

such as beaver, muskrat and mink to control 

levee damage); hiking and walking; wateroriented recreation such as motorized 

boating, canoeing, kayaking, waterskiing, 

house-boating, fishing and swimming/

sunbathing; horseback riding; jogging; 

bicycling; ultralight flying; helicopter 

training; fruit and nut gathering; picnicking 

and camping; and natural history plant 

collecting.

Socioeconomic Demographics

The Refuge is located within Sacramento 

County, bounded by the city of Elk Grove 

on the east, and 15 miles south of downtown 

Sacramento. Sacramento County’s 

population was estimated at over 1.36 million 

in 2005 (USCB 2006) and is projected to 

grow by almost 0.5 million by 2025 (SACOG 

2000). Sacramento is by far the biggest city 

in the county; and even though the Greater 

Sacramento Region includes portions 

of five other counties, 65 percent of the 

city’s population lives within Sacramento 

County. By percentage, Elk Grove was the 

fastest growing large U.S. city, between 

2004 and 2005 (USDOC 2006). Elk Grove 

incorporated in 2000 with a population of 

81,400 (SACOG 2000) and had reached 

112,338 by July, 2005 (USDOC 2006).

 

In 2004, there were an estimated 649,782 

citizens in the labor force in Sacramento 

County (ACS 2004). In 2005 unemployment 

averaged 4.8 percent and is projected to 

decline in 2006 to 4.6 percent (SFP 2006). 

The sectors of the economy accounting for 

the largest numbers of jobs in the county in 

2004 were: management, professional and 

related occupations (35 percent); sales and 

office occupations (31 percent) and service 

occupations (15 percent) (ACS 2004). In 

2004 Sacramento County per-capita income 

averaged $23,589 and median family income 

averaged $57,488 (ACS 2004). Of people 

over the age of 25, 16 percent did not have a 

high school diploma, 23 percent had a high 

school diploma or equivalency, 19 percent 

attained a bachelor’s degree and 8 percent 

attained a graduate or professional degree 

(ACS 2004). In 2004, approximately 10 

percent of Sacramento County residents 

were living in poverty (ACS 2004). 

The largest age group distributions in 

Sacramento county are: between 25 and 

44 years old (30 percent); under 18 (28 

percent) and between 45 and 64 (22 percent) 

(ACS 2004). The racial compositions of 

Sacramento County and the city of Elk 

Grove are relatively diverse. Sacramento 

County’s population is composed of 54.4 

percent Caucasians, 16.1 percent Hispanics, 

12.9 percent Asians and 10.4 percent African 

Americans (ACS 2004). The most recent 

statistics available for Elk Grove, from 

2000, show that Elk Grove has a slightly 

higher percentage of Asian people (17.6 

percent) and slightly less African Americans, 

Hispanics and Caucasians when compared to 

Sacramento County in the aggregate (USCB 

2000). In Sacramento County there was 

an estimated 181,077 households with one 

or more people under the age of 18, in 2004 

(ACS 2004). 

Despite increasing urbanization, agriculture 

continues to be an important economic 

sector in Sacramento County. Sacramento 

County ranked 27th, out of 58 counties, in 

the State for gross value of agricultural 

production for 2002-2003 (CASS 2004). 

The county’s top ten farm commodities 

in 2002 were grapes, milk, nursery stock, 

pears, poultry, vegetable crops, rice, cattle, 

corn and livestock (CASS 2004). While 

agriculture continued to be an important 

sector of the economy, 0.92 percent of prime 

farmland and 5.05 percent of agricultural 

land was converted to urban and build-up 

uses between 1988 and 1998 (Kuminoff et al. 

2000). 

The median home price in Sacramento 

County jumped to $287,672 by 2004 (ACS 

2004) and has continued to rise, reaching 

$360,000 by April of 2006 (CLMI 2006). 

Housing units in the county are projected 

to increase from 473,211 in 2000 to 662,004 

in 2025 (SACOG 2000). Of the increase, 45 

percent will occur in unincorporated areas, 

and 25 percent in the city of Sacramento, but 

fully 20 percent of the increase is projected 

to occur in Elk Grove where housing units 
54 Stone Lakes NWR Comprehensive Conservation Plan

increased from 24,817 in 2000 (SACOG 2000) 

to 66,733 in 2005 (CEG 2006).

Cultural Resources

Cultural Resources and Ethnographic 

Background 

Cultural resources include a variety of links 

to past cultures, such as physical remains, 

sites, objects, records, oral histories and 

traditional culture, but can also include 

landscapes, plants, animals, sacred locations 

and traditional cultural properties that play 

a role in the traditional community. Other 

historic sites represent a wide variety 

of activities, including homesteading 

and settlement, trade, transportation, 

agriculture and ranching. 

Most of the recorded cultural resources at 

the Refuge are archaeological sites linked 

with American Indian occupation that 

include large village sites, small seasonally 

occupied camps, sites with burials and sites 

considered sacred. The material remains 

of historic activities within the project 

boundary may include standing structures 

and foundations, still-occupied dwellings, 

abandoned trails, ferry sites, extant 

roadways and railroad lines.

The Plains Miwok formerly occupied the 

lands now within the approved Refuge 

boundary. The Refuge contains a rich array 

of Plains Miwok cultural history because its 

abundant flora and fauna made it a suitable 

place for humans. Before the area was 

settled by Euroamericans, the Plains Miwok 

territory extended from north of the lower 

reaches of the Cosumnes River to south of 

the lower reach of the Mokelumne River, 

along both sides of the Sacramento River 

and southwest to the vicinity of Mt Diablo in 

Contra Costa County. The eastern boundary 

of their territory was the foothills of the 

Sierra Nevada, which they shared with the 

Central Sierra Miwok (Levy 1978, Service 

1992). 

Typical of the surrounding Central 

California groups, the political organization 

of the Plains Miwok is believed to have 

centered around small tribelets. Each 

tribelet was essentially sedentary and 

occupied a place more or less continuously 

for generations. Resources were variably 

controlled with acorn and hunting lands 

considered communal, while seed tracts 

and fishing stations could be individually 

allocated in accordance with inherited use 

rights for one or more seasons. The tribelets 

also used seasonal camps to exploit seasonal 

resources, such as salmon, acorns, etc. 

(Tremaine 1997, Kroeber 1932, Bennyhoff 

1977).

Numerous Plains Miwok village locations 

were identified during the waning years of 

traditional American Indian inhabitation of 

the region. Major village sites are plotted 

along the Sacramento, Mokelumne and 

Cosumnes rivers. Additionally, several 

locations in Sacramento County have been 

identified as sacred by the Native American 

Heritage Commission. The “Hulpoomne” 

appears to be the nearest known “tribe” 

associated with the north portion of the 

Refuge, being associated with a principal 

village in the area where the town of 

Freeport now stands (Merriam 1907). 

Today, descendants of the Plains Miwok 

continue to have ties to their ancestral lands. 

Known cultural sites on and off Refuge lands 

have been identified and efforts have been 

made to work with tribal representatives 

to restore native habitats while preserving 

these sites. In some cases and at the 

request of tribal representatives, previouslydisturbed archeological sites have been 

capped with layers of soil and vegetation 

to help prevent human remains and other 

objects from being exposed on the surface. 

The comprehensive conservation planning 

process gives us the opportunity to plan for 

the future of the Refuge, working to protect 

these important resources and providing a 

link to the past for current generations of 

Plains Miwok. 

Historic Setting 

Spanish explorers arriving in the 1700s were 

the first people other than American Indians 

to enter the Sacramento Valley area. For 

the most part, the region was little affected 

by Spanish occupation, being removed from 

the missions’ sphere of influence. Land in 
Stone Lakes NWR Comprehensive Conservation Plan 55

the Sacramento Valley was not claimed for 

private ownership until Mexican land grants 

were issued in the 1830s. The Rio Ojotska 

land grant, issued in 1833 to J.B.R. Cooper, 

was the earliest land grant given in the area; 

however, the recipient failed to lay claim 

to the land and renounced the grant the 

following year (USFWS 1992).

New Helvetia, established by John A. Sutter 

in 1839 near the present site of Sacramento, 

was the first Euroamerican settlement in 

the valley. Sutter obtained 11 leagues of 

land through a grant from the Mexican 

government, which approved of Sutter’s 

plan to build a fort and establish order on 

the edges of their frontier. Sutter’s Fort 

was founded with goods purchased from the 

Russians when Fort Ross was abandoned in 

1841. A large number of horses and cattle 

were brought to Sutter’s Fort, along with a 

cannon and several pieces of artillery. These 

accoutrements gave the fort a military 

appearance, which undoubtedly discouraged 

skirmishes between the settlers and 

American Indians (USFWS 1992).

Lands along the Cosumnes River, northeast 

of the Refuge, were claimed in 1844 by 

two employees of Sutter. At the time, the 

Cosumnes area was “thickly populated 

by Indians” (USFWS 1992). The land, 

which was claimed to graze cattle, was 

called Rancho Omochumnes after the local 

American Indian tribelet. Another land 

grant, Sanjon de los Moquelumnes, included 

the southeastern portion of the Refuge; this 

land grant was also named after a Plains 

Miwok tribelet.

In 1848, California and the Sacramento 

Valley were changed forever by the 

discovery of gold in the Sierra Nevada 

foothills. Until that time, most of California 

had been unaffected by Euroamerican 

settlement. With the discovery of gold, 

thousands of miners entered the state. 

Thousands of settlers soon followed 

the miners. Sacramento was the main 

community, surrounded by dozens of 

smaller settlements. In the beginning, 

the locations of early towns coincided with 

mining activities. Probably only limited 

mining occurred in the vicinity of the Refuge 

because of the scarcity of gold-bearing 

gravels at such low elevations. Later, as 

agricultural pursuits replaced mining, 

farming communities appeared. By the 

1860s, agricultural enterprises were well 

established in the Sacramento Valley and the 

Delta region. A variety of crops were grown 

on and west of the Refuge while areas to the 

east were used for mixed agriculture and to 

raise livestock. Towns that were established 

near the Refuge include Franklin, 

Bruceville, Locke, Sheldon and Wilton.

Archeology 

Requests have been submitted to the 

North Central Information Center of the 

California Archaeological Inventory for 

information regarding the types and location 

of archeological sites on and in the vicinity 

of the Refuge. Historic and ethnographic 

sources were also reviewed for information 

pertaining to the area.

Types of Archeological Sites. Intensive 

prehistoric and historic habitation and use 

in the Sacramento area has resulted in a 

large and diverse archeological resource 

base. Over 450 archeological sites have 

been recorded in Sacramento County. Many 

sites have been recorded, although most 

lands within the approved Refuge boundary 

have not been surveyed systematically for 

cultural resources. 

Most of the recorded sites within the 

vicinity of the Refuge are prehistoric in 

nature. Although this is partly because 

prehistoric site density is greater than 

historic site density in the Refuge area, it 

is also because most archeologists working 

in the area did not record historic sites 

until quite recently. Sites associated with 

American Indian occupation include large 

sites, small, seasonally occupied camps, sites 

with burials and sites that were considered 

sacred. Historic sites represent a wide 

variety of activities, including homesteading 

and settlement, trade, transportation, 

agriculture and ranching. The material 

remains of these activities probably include 

standing structures and foundation, still 

occupied dwellings, abandoned trails and 

ferry sites, extant roadways and railroad 
56 Stone Lakes NWR Comprehensive Conservation Plan

lines.

Location of Archeological Sites. Both 

prehistoric and historic sites within and 

around the Refuge tend to be located on 

high ground near permanent water sources. 

Determining areas of historic sensitivity 

is difficult, however, because of the lack of 

identified historic period sites within the 

Refuge. For the most part, early historic 

settlements (before the establishment of 

reliable flood control measures) were located 

on prehistoric sites. In fact, it is common 

to find a prehistoric midden site under a 

historic dwelling because American Indians 

often chose to live on topographic high 

points. American Indian habitation sites 

became even higher points of land as their 

refuse accumulated over hundreds or even 

thousands of years of occupation, and these 

mounds were attractive building locations 

for early settlers. In addition to topographic 

high points, historic remains should be 

expected near early settlement locations, 

along railroad lines and near ferry sites.

Many prehistoric archeological sites have 

been identified along major drainages, such 

as the Mokelumne and Cosumnes rivers and 

Laguna, Skunk, Badger and Deer creeks. 

Many unidentified sites are probably present 

on these drainages although intensive, 

systematic surveys have never been done. 

Additional areas of prehistoric sensitivity 

include the lands around Beach, North, and 

South Stone lakes and Snodgrass and Bear 

sloughs.

Land Use 

Natural biologic communities presently 

occurring within the entire approved 

Refuge project boundary encompass a 

total of 8,158 acres and include: annual 

grasslands (62 percent), seasonal wetlands 

(14 percent), perennial wetlands (5 percent), 

riparian forest and scrub shrub (8 percent), 

deepwater aquatic habitat (9 percent) 

and oak woodlands (2 percent). Existing 

agricultural cover types within the Refuge 

occupy an additional 8,740 acres and are 

comprised of: corn (28 percent), pasture 

(21 percent), range (17 percent), wheat (8 

percent), sugar beets (8 percent), grapes (7 

percent), other field crops (4 percent), pears 

(2 percent) and tomatoes (1 percent). 

Adjacent lands in this region are shifting 

from low density, rural, residential homes 

and structures, agriculture, and recreational 

areas to medium density single family 

suburban tract homes, master-planned 

communities and vineyards (B. Treiterer, 

USFWS, pers. comm.)

Wilderness and Other Special 

Management Areas 

As required by Service planning policy, 

a wilderness review (Appendix E) was 

conducted for the Refuge. None of the 

Refuge lands were eligible for wilderness 

designation.

Current Management Practices

The primary management focus of the 

Refuge is enhancing, restoring and 

maintaining wetlands, riparian woodlands, 

grasslands and valuable agricultural lands. 

Wetland habitats include permanent and 

seasonal wetlands, including vernal pools, 

riparian woodlands, open water and aquatic 

beds.

Wetlands

Water Management. As an integral part of 

the Refuge program, the Service manages 

water on seasonal and permanent wetlands 

on the South Stone Lake, Headquarters and 

Beach Lake units totaling approximately 

335 acres. Sources of water for managed 

Refuge wetland units include SP Cut, Lower 

Beach Lake, Sacramento Drainage Canal 

and South Stone Lake. A total of seven 

surface pumping stations draw water from 

Refuge waterways to manage wetland 

impoundments on the Refuge. Water control 

structures (i.e., screw gates) are also used 

to manage water entering other permanent 

wetlands areas, such as North Stone Lake 

and Parker Slough and portions of the Sun 

River property. The overall water flow in the 

SP Cut is controlled by screw and flap gates 

passing under Lambert Bridge, upstream 

drainage, groundwater levels and irrigation 

return flows. 

Flood up, drawdown and summer irrigations 
Stone Lakes NWR Comprehensive Conservation Plan 57

are planned to provide habitat for migrating, 

wintering and breeding water birds. Timing 

of flood up is constrained to varying degrees 

by the amount of water available under 

appropriative and riparian water rights in 

any given year and to minimize mosquito 

production. 

Permanent Wetlands. Permanent wetlands 

are managed to provide brood rearing 

habitat during the summer months for 

waterfowl and other waterbirds and year 

round habitat for other species, including 

bitterns, herons and marsh wrens. Periodic 

draw downs of the permanent wetlands on 

the Beach Lake, Headquarters and South 

Stone Lake units are done when vegetation, 

such as cattails and tules, covers more than 

75 percent of the surface area and to control 

undesirable fish species such as carp. These 

treatments occur approximately every three 

to five years. Not more than three out of 

the five permanent wetland impoundments 

on these units are drawn down in any given 

year, in order to maintain habitat for the 

federally-threatened giant garter snake and 

summer resident birds. In other permanent 

wetlands, such as Parker Slough, North 

Stone Lake, and the Sun River property, 

water levels can be manipulated using screw 

gates to lower levels, but not completely 

de-water wetlands. In these situations, the 

goals are to stimulate growth of desirable 

moist soil plants along pond edges and allow 

for some control of dense vegetation, if 

necessary. 

Seasonal Wetlands. Seasonal wetlands are 

managed to provide feeding and loafing 

habitat for the thousands of migratory 

waterbirds that winter in the Central Valley 

and make use of the Beach-Stone Lakes 

Basin. During years with no restrictions 

on water use, flood ups begin in early to 

mid-September and continue through 

mid-October. To minimize mosquito 

production, impoundments are rapidly 

filled to a maximum depth of one to two 

feet. Occasional pumping may be required 

during the winter if rainfall levels are below 

normal. Drawdowns commence in early 

April and continue through mid-June. 

Varying the draw down schedule in wetland 

units stimulates production of different 

plants. Early draw downs favor grasses, 

such as swamp timothy and watergrass; 

late drawdowns favor smartweeds and some 

undesirable plants, such as cocklebur. Late 

drawdowns occur in one or two wetland 

units per year to provide habitat for nesting 

shorebirds, including black-necked stilts 

(Himantopus mexicanus), American avocets 

(Recurvirostra Americana) and Wilson’s 

phalaropes (Phalaropus tricolor). Summer 

irrigations are designed to stimulate the 

growth of high quality foods for waterfowl, 

such as swamp timothy and watergrass. 

These are done in late July and early 

August when the unit is flooded to a depth 

of 12 inches and then drawn down. Close 

coordination with the Sacramento/Yolo 

Mosquito Vector Control District is essential 

to minimize mosquito production on 

managed wetlands.

SP Cut. Water levels in the SP Cut are 

controlled by screw and flap gates passing 

under Lambert Bridge, upstream drainage, 

groundwater levels and irrigation return 

flows. Through informal agreement with 

Sacramento County Department of Water 

Resources, the screw gate on the Lambert 

Bridge flood control structure is operated by 

a local landowner to manage availability of 

upstream water for irrigation and wetland 

management. Water levels are generally 

higher during the summer months when the 

gate at Lambert Bridge is open and farmers 

upstream are irrigating crops. During 

the winter, water levels are determined by 

rainfall levels and drainage entering from 

upstream. During large rainfall events, 

water enters SP Cut when floodwaters 

overtop the Morrison Creek dam at the 

north end of Lower Beach Lake. 

North Stone Lake. North Stone Lake 

is roughly 260 acres in size with depths 

ranging from 0.5 feet to 8.0 feet. Water 

enters the lake via concrete culverts under 

Interstate-5 that bring water from upstream 

developed areas to the east and from SP Cut 

to the west, through a single pipe fitted with 

a screw gate. Water levels in the lake can be 

manipulated to a limited degree (12 inches 

maximum) by opening or closing this screw 
58 Stone Lakes NWR Comprehensive Conservation Plan

gate, depending on water fluctuations in the 

SP Cut. There are no control structures on 

the Interstate-5 culverts. 

South Stone Lake. Water levels in various 

parts of South Stone Lake fluctuate with 

levels in SP Cut and tidal influences from 

downstream of Lambert Bridge. As with 

North Stone Lake, water levels are highest 

during the summer irrigation months 

and winter rainfall months. Except for 

requesting opening of the screw gate at 

Lambert Bridge, Refuge staff have little 

control over water levels in South Stone 

Lake.

Habitat Manipulations. Managed 

wetlands are dynamic systems that require 

periodic habitat manipulations to maintain 

a desired successional stage, optimal for 

feeding, loafing, breeding waterfowl and 

waterbirds. Mowing, prescribed burning, 

discing and noxious weed control during late 

summer are all part of efforts to manage less 

desirable vegetation with limited food value 

for migratory waterbirds, such as cocklebur 

and spike rushes. These activities also 

improve conditions for grasses and forbs to 

grow, such as watergrass, swamp timothy, 

smartweeds as well as other desirable 

vegetation, such as bulrush, buttonbush 

and willow. Each unit is evaluated annually 

to determine the need for manipulations. 

Permanent wetland units are disced every 

three to five years to maintain an equal 

ratio of open water to vegetation. Seasonal 

wetlands are disced or mowed every other 

year, depending on vegetation response. 

The perimeter of each wetland is disced to 

enhance access by mosquito fish and water 

management.

Mosquito Control

The Refuge staff works closely with the 

Sacramento/Yolo Mosquito Vector Control 

District (SYMVCD) to reduce or eliminate 

production of mosquitoes on the Refuge. In 

accordance with the EIS (USFWS 1992), 

the Refuge entered into an MOU with 

SYMVCD in 1993. This MOU outlines an 

effective mosquito suppression program 

that includes biological and chemical 

controls to be used on the Refuge, wetland 

design and water level and vegetation 

management recommendations and research 

partnerships. Biological controls include 

the placement of mosquito fish and guppies 

(Poecilia reticulate) in permanent and 

seasonal wetlands and the use of Bacillus 

thuringiensis israeliensis (Bti) and B. 

sphaericus, which are effective at controlling 

certain life stages of mosquito larvae with 

minimal non-target organism impacts. Any 

pesticides to be used on the Refuge must be 

approved by the Service prior to the onset of 

mosquito season in early spring. Pesticides 

may target mosquito larvae and adults and 

may include aerial applications, as well as 

ultra-low volume ground application. In 

keeping with the MOU, the Refuge consults 

with SYMVCD to ensure wetlands are 

designed to minimize mosquito habitat. 

For example, berms along some managed 

wetland units are graded with a slope of 

1.5-2.0 feet horizontal to 1.0 foot vertical 

to limit the growth of marginal vegetation. 

Furthermore, the perimeters of seasonal 

wetlands may be disced to enhance access by 

foraging mosquito fish to larvae. Wetlands 

are also designed and constructed to allow 

for rapid flooding and draw down.

Riparian

Agricultural conversion, water conveyance, 

and flood control, and other changes in land 

use have eliminated much of the original 

riparian and oak woodland habitat from 

the Beach-Stone Lakes Basin. Overall, the 

Central Valley has lost over 95 percent of 

its wooded riparian habitats. Within the 

approved Refuge boundary, the widths of 

riparian forest corridors vary from 10-300 

feet wide along Morrison Creek, SP Cut, 

Parker Slough, the south arm and smaller 

branches of North Stone Lake, and South 

Stone Lake (see Figure 5, Vegetation Map). 

The only mature valley oak forest remaining 

in the basin exists along Morrison Creek. 

Restoration efforts on the Beach Lake, 

North Stone Lake, Headquarters and South 

Stone Lake units have expanded riparian 

zones by 100-120 acres. 

Restoration practices include planting a 

variety of riparian trees, such as Fremont 

cottonwood, willow, box elder, sycamore,, 
Stone Lakes NWR Comprehensive Conservation Plan 59

valley oak and associated understory shrubs 

and grasses and then providing supplemental 

irrigation and weeding for a period of three to 

five years to facilitate plant establishment. In 

the case of valley oaks, both planting acorns 

with no watering and seedlings with watering 

have been used with success. Choosing 

an appropriate site based on soil type and 

elevation is the most important aspect of a 

successful restoration project. 

Grasslands 

Grasslands once covered vast stretches of 

the Central Valley, supporting extirpated 

species, such as pronghorn antelope, tule elk 

(Cervus elaphus nannodes), grizzly bear and 

millions of waterfowl and other migratory 

birds. These grasslands supported seasonal 

wetlands such as vernal pools and wet 

meadows populated by perennial and annual 

grasses. Over 98 percent of Central Valley 

native grasslands have been converted 

to agriculture and urban development or 

displaced by exotic vegetation. . Many 

native annual grassland species no longer 

occur and have been replaced by nonnative 

annuals such as annual rye. The remaining 

grasslands are now a mix of native and 

nonnative species.

The North Stone Lake Unit of the Refuge 

supports one of the only remaining 

continuous tracts of un-leveled grasslands 

in the eastern Sacramento-San Joaquin 

Delta region, with approximately 1,900 

acres of annual and perennial grasslands. 

Preservation of this remnant grassland 

topography is a high priority. Other small 

(one to 21 acres) areas exist on the Beach 

Lake and Headquarters units. General 

management goals for the North Stone 

Lake Unit are to: maintain and expand 

existing native grasses, such as creeping 

wild rye (Leymus triticoides), meadow 

barley (Hordeum brachyantherum), and 

sedges; minimize the fire hazard posed 

by accumulated dead grasses; control 

the spread of noxious weeds; and provide 

habitats for grassland-dependent species, 

including greater sandhill cranes, arctic 

nesting geese, white-faced ibises, long-billed 

curlews, western meadowlarks, horned 

larks, and birds of prey, including Swainson’s 

hawks, burrowing owls, and northern 

harriers. These management goals are 

being accomplished through implementation 

of a cattle grazing program, small-scale 

prescribed burning, and aggressive noxious 

weed control.

The Refuge grazing 

program on the 

North Stone Lake 

Unit consists of 

running cattle on 

the dry pasture 

from November 

through mid-June, 

until annual grasses 

turn brown. Some 

cattle are then moved 

to the 172 acres of 

irrigated pasture on 

the unit from June 

through October. 

Cattle stocking rates 

vary in the five dry pastures depending on 

rainfall, timing, quantity and frequency, with 

a target of 1,500-2,000 pounds of Residual 

Dry Matter (RDM) in three of the five 

pastures and 2,000-4,000 pounds of RDM in 

the remaining two pastures. The irrigated 

pastures are stocked at a rate of one animal 

unit month (AUM), which is the amount of 

forage needed by a cow and her suckling 

calf for one month, per one to two acres. 

Following a 10-year period during which 

grazing had been curtailed on the North 

Stone Lake Unit, use by sandhill cranes, 

long-billed curlews, white-fronted geese, and 

other waterfowl has increased substantially 

on the unit after the Refuge re-introduced a 

grazing program in 1999. Excluding cattle 

from the majority of riparian areas through 

fencing was completed in 2003. Other 

measures to improve management of the unit 

will include developing alternative watering 

sources ,erosion control measures near the 

irrigated pastures, noxious weed control and 

continued monitoring of wildlife responses. 

The Refuge holds title to a conservation 

easement on the 1,400-acre Wetland 

Preserve Unit that supports a mixture of 

natural and man made vernal pools and 

seasonal wetlands. Recent studies at the 

General restoration 

goals for the 

grasslands on 

the North Stone 

Lake Unit are 

to: maintain and 

expand existing 

native grasses, 

decrease the fire 

danger, control 

noxious weeds and 

provide habitat for a 

variety of grassland 

dependent species 

like this Swainson’s 

hawk.

Photo by USFWS 
60 Stone Lakes NWR Comprehensive Conservation Plan

Cosumnes River Preserve (J. Marty, TNC, 

pers. comm.) indicate that a managed 

grazing program is most effective at 

maintaining and enhancing vernal pool plant 

and animal species. Grazing conducted by 

the landowner from November through 

June on the preserve results in a RDM rate 

of 600 to 800 pounds and is ideal to reduce 

competition between vernal pool plants 

and nonnative grasses, such as annual rye 

grass, and noxious weeds, such as yellow 

starthistle (Centaurea solstitialis). Refuge 

staff are working with representatives of the 

landowner, AKT Development Corporation, 

to develop a grazing program that will 

protect and enhance seasonal wetlands on 

the preserve. 

Weed Control

Since 1995, the Refuge has adopted an active 

aquatic and terrestrial weed management 

program in the Beach-Stone Lakes Basin, 

particularly as a founding member of the 

Stone Lakes Water Hyacinth Control 

Group. The Refuge conducts treatments 

for control of water hyacinth under a 

Statewide National Pollution Discharge 

Elimination System (NPDES) General 

Permit (No. CAG990005) for discharge of 

aquatic pesticides. The Refuge and SRCSD 

utilize Reward (Diquat) and Aquamaster 

(glyphosphate) to control water hyacinth 

in the basin. Another aquatic species, 

Brazilian elodea (Egeria densa), is also 

abundant in waterways and may emerge as 

a management concern as opportunities for 

recreational boating are developed on the 

Refuge. 

The Refuge Integrated Pest Management 

approach used to control weeds relies 

on burning, mowing, grazing, discing 

and herbicide applications. Due to the 

persistence and abundance of most 

weeds in the environment and regulatory 

constraints on use of fire, chemical 

applications are the only currently 

effective method for controlling water 

hyacinth, perennial pepperweed (Lepidium 

latifolium) and yellow star thistle. The 

Refuge uses Transline and Telar to 

control yellow star thistle and perennial 

pepperweed, respectively. Mechanical 

control methods tend to spread, rather 

than control, perennial pepperweed. 

Potential biological control organisms, 

including water hyacinth-eating weevils 

(Neochitina spp.) and moths (Sameodes 

albiguttlilis), have been introduced into 

the Delta through a cooperative program 

with the U.S. Department of Agriculture, 

Agricultural Research Service (USDAARS) and California Department of Food 

and Agriculture (CDFA) to evaluate 

control of water hyacinth. Unfortunately, 

these biological control agents have 

not been affective in reducing stands of 

water hyacinth. Given the vast amounts 

of hyacinth produced each year on the 

Refuge and its inaccessibility to equipment, 

mechanical control is not feasible. 

Mechanical removal in isolated water 

ways would be prohibitively expensive, 

costing an estimated $80,000 annually 

and accessing sites with heavy equipment 

would likely cause significant impacts to 

sensitive habitats. Non-chemical methods to 

prevent the spread of water hyacinth include 

deploying log booms at strategic locations 

to prevent spread, screening culverts to 

prevent re-introduction and removing 

water hyacinth from small water bodies by 

hand. The Refuge also participates in the 

Sacramento Weed Abatement Team which 

is coordinated by the Sacramento County 

Agricultural Commission.

Farming Program

A variety of migratory birds, including 

waterfowl, long-billed curlew, black-bellied 

plover, white-faced ibis and sandhill cranes, 

feed on waste grain and invertebrates 

remaining in agricultural fields after 

harvest. These migratory birds depend 

on farm fields of small grains, alfalfa, 

tomatoes, etc. for a marked portion of their 

diet. Therefore, it is vital that the Service, 

private landowners, and Sacramento County 

cooperate to maintain viable “wildlife 

friendly” agriculture in the vicinity of the 

Refuge. Except for the grazing programs 

that the Refuge oversees, cooperative 

farming on Refuge lands currently is limited 

to the Headquarters Unit. To date, the goal 

of the farming program has been to maintain 

the fields in corn, wheat, safflower, or grass 
Stone Lakes NWR Comprehensive Conservation Plan 61

to provide habitat for wildlife and control 

weeds until a larger scale restoration project 

is implemented.

Monitoring and Surveys

A variety of surveys and studies have been 

conducted by Service staff, volunteers 

and students on the Refuge since its 

establishment. These studies are primarily 

intended to evaluate the effectiveness of 

management activities and monitor the 

status of biological resources. A summary 

of ongoing surveys and studies and their 

objectives follows.

Colonial waterbird survey. Rookeries 

of nesting great blue heron, great 

egrets, and double-crested cormorants 

are monitored yearly to determine 

abundance, distribution and nesting 

success. 

Landbird monitoring program. A 

cooperative mist netting and bird 

banding program is conducted in 

selected areas with SYMVCD to 

monitor and document bird diversity 

and relative abundance. The program 

is also investigating the role of wild bird 

populations as reservoirs for mosquitoborne diseases such as Western equine 

encephalitis virus, St. Louis encephalitis 

virus and west Nile virus. 

Modesto song sparrow study. As part 

of the landbird banding program, song 

sparrows are also color banded on the 

South Stone Lake Unit in an ongoing 

effort to determine nesting success and 

survival of young.

Weekly waterfowl survey, October 

through May. Waterbird (waterfowl, 

shorebirds and cranes) counts are done 

weekly during the fall, winter and spring 

to determine population trends and use 

patterns.

Plant surveys. Vegetation in moist soil 

wetlands is qualitatively surveyed each 

spring to guide management actions 

such as discing, mowing and timing of 

summer irrigations. 

Noxious weed surveys. Refuge units 

are surveyed and mapped with GPS 

equipment to monitor noxious weeds 

such as yellow starthistle, perennial 

pepperweed and water hyacinth.

•

•

•

•

•

•

Pasture monitoring A residual dry 

matter survey (measure of the amount 

of dry grass remaining after the growing 

season) is conducted annually to adjust 

grazing rates for the upcoming year.

The following studies have been 

completed primarily by graduate 

students on the Refuge:

Western pond turtle survey. Determined 

turtle survival and reproductive success.

Native grass. Determined effects of 

various treatments (e.g., burning, grazing 

and no treatment) on three species of 

native grasses on the North Stone Lake 

Unit.

Nitrogen. Determined the role increased 

nitrogen levels may play in exotic weed 

expansions along freeway corridors.

Sunflower moth. Evaluating the 

relationship between the California 

sunflower and its parasitoids.

Bats. Conducted presence or absence 

surveys on selected sites on the Refuge.

Aquatic surveys. Conducted fish, 

amphibian, and reptile surveys to 

determine presence and absence of 

various species.

Further refinement of survey and 

monitoring protocol for the Refuge is 

needed. Additional baseline inventories 

need to be completed and a relational 

database should be developed to store and 

access monitoring and inventory data.

•

•

•

•

•

•

•

•

A cooperative mist 

netting and bird 

banding program 

is conducted in 

selected areas with 

the SacramentoYolo Mosquito 

and Vector Control 

District to monitor 

and document 

the diversity and 

relative abundance 

of bird species, 

such as this blue 

grosbeak, and to 

evaluate their role 

in the transmission 

of mosquito-borne 

viruses.

Photo by USFWS
62 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 63

4 Challenges

Invasive Species

As defined in Executive Order 13112, an 

invasive species is an alien species whose 

introduction does or is likely to cause 

economic or environmental harm or harm to 

human health. Invasive species can impact 

human health, interfere with agriculture and 

aquaculture, interfere with water delivery, 

increase flooding and erosion, block access 

to water ways, decrease habitat for native 

plants and animals and compete with native 

species for resources. Invasive species 

are one of the most critical nationwide 

challenges facing national wildlife refuges 

(NWRA 2002). The Service and other 

bureaus within the Department of the 

Interior have been working to eradicate 

invasive species on Federal lands and are 

partnering with State agencies and local 

organizations to restore ecosystems with 

native plants and species. By 1998, the 

battle against invasive species was costing 

the Refuge System an estimated $13 million 

per year (NWRA 2002). By 2002 a $150 

million backlog of critical invasive species 

projects had been identified within the 

Refuge System (NWRA 2002). Most current 

management practices are aimed at control 

and eradication of existing invasive species; 

much work remains to prevent introduction 

of additional invasive species, educate 

the public and to fund more research and 

monitoring.

A large number of invasive species now 

reside on the Refuge. Vertebrate invasive 

species found on the Refuge that are well 

established in the region include European 

starlings (Sturnus vulgaris), rock doves 

(Columba livia), American bullfrogs redeared sliders, feral dogs (Canis lupus 

familiaris), feral cats (Felis silvestris), 

black rats (Rattus rattus), Norway rats 

(Rattus norvegicus) and house mice 

(Mus musculus). The majority of fishes 

occurring in Sacramento-San Joaquin 

Delta and Refuge waterbodies are nonnative, including carp, catfish, sunfish and 

largemouth bass. Except for capture of 

feral dogs and cats and localized reductions 

of rodents near buildings and carp from 

wetland impoundments, no active control 

of these species is currently conducted or 

planned. As urban areas expand, we expect 

to see increases in feral dogs and cats, 

rock doves and great basin Canada geese. 

Preliminary studies at the Cosumnes River 

Preserve indicate black rats are negatively 

affecting reproductive success in a variety 

of songbirds nesting in mature valley oak 

riparian forest. Invasive invertebrates 

found on the Refuge, such as various species 

of mosquitoes and mitten crab (Eriocheir 

sinensis), may act as hosts to various 

diseases. Control of mosquito populations 

is addressed in Chapter 3 under Current 

Management. Mosquitoes are a vector for 

western equine encephalomyelitis virus. 

St Louis encephalitis and west Nile virus 

that can cause disease in humans. Mitten 

crabs can act as a host to the Asian lung 

fluke (Paragonimus westermani), which can 

cause disease in humans and other mammals 

if consumed without thorough cooking 

(ANSTF 2003). 

Methods used to control invasive weeds 

include chemical, mechanical (including 

mowing, discing and hand removal) 

and biological control. The majority of 

grasslands on the Refuge and throughout 

California are now composed of nonnative 

annual grasses, such as annual rye, soft 

chess (Bromus hordeaceus), wild oats 

and Mediterranean barley (Hordeum 

marinum). Himalayan blackberries (Rubus 

armeniacus) are prevalent in riparian zones 

and along waterways. Invasive tree species 
64 Stone Lakes NWR Comprehensive Conservation Plan

on the Refuge include black locust (Robinia 

pseudoacacia) and osage orange (Maclura 

pomifera). Many of these invasive species 

have replaced native vegetation, but are 

so well established that eradication would 

be nearly impossible. Current control and 

eradication efforts concentrate on three 

noxious weeds that require immediate 

attention (Table 1). Other species being 

considered for monitoring, control and 

eradication from grassland, aquatic, and 

riparian habitats include: medusahead grass 

(Taeniatherum caput-medusae), barbed 

goat grass (Aegilops triuncialis), Brazilian 

elodea, and giant reed (Arundo donax). 

Basin Hydrology and Water Quality

Floodplain Conditions 

The hydrologic regime and configuration of 

the 100-year floodplain in the Beach-Stone 

Lakes Basin have been dramatically altered 

when compared with historic pre-settlement 

conditions. Changes to the landscape have 

included: (1) completion of the Sacramento 

River levee system and Sacramento Flood 

Control Project; (2) dam placement on the 

Mokelumne River; (3) construction of the 

Southern Pacific Railroad; (4) reclamation of 

tracts and islands in the basin for farming; 

and (5) constricting of downstream channel 

capacities due to raising of levees. 

The approved Refuge boundary lies 

entirely within the 100-year floodplain of 

Morrison Creek and the Cosumnes and 

Mokelumne rivers and the current 100-year 

flood elevation is 16.00 feet above mean sea 

level. Damaging floods have occurred in 

the Beach-Stone Lakes basin an average of 

one out of every three years (USACE 1987, 

Hart 1999). Extensive flooding occurred in 

14 of the last 40 years. The primary source 

of water during flood events is from the 

accumulated flows of the 192 square mile 

watershed of the Morrison Creek Stream 

Group (Morrison, Elder, Unionhouse, Florin 

and Laguna creeks). During high water 

events, Morrison Creek drains from east 

to west, then south through Beach Lake, 

North Stone Lake, and South Stone and 

finally through the Lambert Road bridge 

to Snodgrass Slough, thence into the 

North Mokelumne River. Alternately or 

concurrently, flood waters may flow south to 

north from the Cosumnes and Mokelumne 

Rivers up Snodgrass Slough and the 

Sacramento Drainage Canal, over the top of 

the Lambert Road bridge and into SP Cut 

Table 1. Invasive Plant Species Targeted for Control on Stone Lakes National Wildlife Refuge.

Common Name Scientific Name **State Noxious Listing Distribution and Origin

perennial pepperweed Lepidium latifolium B waterways, riparian 

restoration sites, grasslands 

and along roadsides 

yellow starthistle Centaurea solstitialis C grasslands, roadsides

water hyacinth Eichhornia crassipes none waterways, permanent 

wetlands, lakes

Brazilian elodea Egeria densa none waterways, permanent 

wetlands, lakes

giant reed Arundo donax none waterways, ditches

black locust Robinia pseudoacacia none ornamental landscapes

osage orange Maclura pomifera none hedgerows, ornamental 

landscapes

medusa head grass Taeniatherum caput-medusae C grasslands

**”B”—Eradication, containment, control or other holding action at the discretion of the commissioner. “C”—State endorsed 

holding action and eradication only when found in a nursery; action to retard spread outside of nurseries at the discretion of the 

commissioner; reject only when found in a cropseed for planting or at the discretion of the commissioner (CDFA 2006).
Stone Lakes NWR Comprehensive Conservation Plan 65

and the Beach-Stone Lakes basin. Cosumnes 

and Mokelumne river flows may also enter 

the basin from the west by backing up along 

and passing under the Western Pacific 

Railroad grade. The flood season normally 

extends from November through April 

(USFWS 1992).

The Refuge receives storm water runoff 

from upstream urban developments, 

including Laguna West, Lakeside and 

Stonelake, which flow into Beach Lake and 

North Stone Lake. Projections are that 

continued urbanization will lead to a loss 

of upstream storage area and a doubling 

of storm water runoff entering the Stone 

Lakes basin. Build-out of the East Franklin, 

Poppy Ridge, Laguna Ridge and Lent Ranch 

projects east of Franklin Boulevard, will 

result in an additional 10,000 acres of urban 

development between Interstate-5 and 

Highway 99. This may lead to increases in 

both the elevation of the 100-year floodplain 

and duration of downstream flooding 

(CEG 2000). Under this scenario, impacts 

are anticipated to Refuge infrastructure, 

habitats and wildlife.

Increases in elevation and duration 

of flooding resulting from upstream 

development may affect the grassland, 

riparian and wetland habitats and associated 

wildlife now using the Refuge. Noxious 

weeds, such as perennial pepperweed, 

yellow star thistle and other species, 

may become more invasive on grassland 

habitats as seed sources are washed into 

the Refuge. Long term monitoring will 

be necessary to document changes in the 

nature of grasslands. Riparian habitats 

may be affected due to prolonged high 

flood water levels, particularly during the 

spring. Conversion of stands of willows 

and cottonwood trees in low lying areas to 

more aquatic habitats may result and the 

composition of seasonal and permanent 

wetlands may change. 

Migratory birds that frequent large 

expanses of open water may benefit 

from these habitat conversions, such as 

white pelicans and tundra swans and the 

composition of local duck populations may 

shift from dabbling ducks, such as mallard 

and northern pintails, to diving ducks, such 

as canvasbacks (Aythya valisineria) and 

lesser scaup (Aythya affinis). Reduction in 

the availability of high ground for high water 

refugia may further impact listed species 

such as the giant garter snake and valley 

elderberry longhorn beetle. 

More frequent and longer flooding events 

could also affect management of the grazing 

program on the North Stone Lake Unit 

of the Refuge. From November through 

mid July, cattle are rotated among five 

pasture units and during heavy rainfall 

events, they are moved from the southern 

to the northern pastures in anticipation of 

flooding. Floodwaters rose 6 inches an hour 

during heavy rains in the winter of 2000, 

making unsafe conditions for driving the 

cattle north. Similar heavy rains during the 

winter of 2005/2006 also required relocation 

of cattle grazing. Increases in storm water 

flows could exacerbate this situation which 

may result in shortening of the grazing 

period.

Flood Control Projects

In addition to ongoing upstream 

development, hydrologic regimes on the 

Refuge may also be affected by new projects 

that could alter the configuration or depth 

of the 100-year floodplain. The hydrology of 

the Mokelumne and Cosumnes rivers and 

Some species that 

frequent large 

expanses of open 

water, such as white 

pelicans, may 

benefit from more 

frequent flooding of 

the Refuge.

Photo by USFWS
66 Stone Lakes NWR Comprehensive Conservation Plan

the Morrison Creek watershed has been 

studied extensively for various potential 

flood control projects by the USACE, 

California Department of Water Resources, 

City of Sacramento and Sacramento County. 

These projects include a recently completed 

project by Sacramento Area Flood Control 

Agency and the USACE to raise and reconfigure levees along Morrison Creek and a 

project by Teichert to realign Laguna Creek 

for gravel extraction, which may decrease 

summertime flows from reaching Beach 

Lake. 

Since the mid-1980s, Sacramento County 

has been exploring the feasibility of 

implementing a flood control project in 

the basin that could reduce the extent of 

the 100-year floodplain and in particular, 

decrease flooding in the community of 

Point Pleasant in southern Sacramento 

County. In 1998, the County Board of 

Supervisors adopted the Beach-Stone 

Lakes Flood Control Plan, outlining county 

policies for reducing flooding in the basin. 

Most recently, the County has convened a 

facilitated private and public stakeholder 

forum to explore alternatives for reducing 

or compensating for flood damages to 

landowners in the Beach-Stone Lakes basin. 

The forum will report back to the County 

Board of Supervisors with the results of 

their deliberations regarding a potential 

regional project to attenuate peak flood flows 

or improve flood conveyance. The County 

will then utilize engineering studies and the 

forum results to prepare a report on key 

findings of this effort. 

Water Quality

Water quality is an important component 

in determining the overall function of the 

Refuge area ecosystem and is a major 

factor in determining the health of wildlife, 

aquatic organisms and fisheries. Water, 

sediment, and biota samples collected from 

eight locations indicate that levels of heavy 

metals, although present, were not sufficient 

to cause deleterious impacts to wildlife; 

however, concentrations of selenium in all 

five waterbodies tested are above levels 

recommended for the protection of aquatic 

life (USFWS 1992). 

The Refuge is virtually surrounded by urban 

and agricultural areas. Environmental 

contaminants on the Refuge or in the area 

have the potential to accumulate on the 

Refuge and affect large numbers of fish 

and wildlife. Agricultural lands to the east, 

south, and southwest are potential sources 

of contaminants to Snodgrass Slough, as 

well as to South and North Stone lakes. 

Many small waterways and seasonal swales 

connect the agricultural lands with the 

Snodgrass Slough and North and South 

Stone lakes. The City of Sacramento is 

another potential contaminant source. 

Morrison Creek runs through southern 

Sacramento prior to entering the north end 

of the Refuge and has been characterized 

by the Environmental Protection Agency 

(EPA) as an impaired waterway because 

of high Diazinon concentrations. The EPA 

found that Diazinon poses unacceptable 

risks to agricultural workers and to birds 

and other wildlife species. Diazinon can 

overstimulate the nervous system, causing 

nausea, dizziness and confusion and at very 

high exposures caused by accidents or major 

spills, it can also cause death. 

 

Additional studies of water quality 

conducted by Service Contaminants staff 

from 1999 to 2000 found that levels of 

pesticides with Diazinon in Morrison Creek 

were sufficient to cause mortality in bioassay 

organisms after rainfall greater than one 

inch. Most likely these pesticides were 

flushed through the stormwater runoff 

drainage system after accumulating on 

lawns and other areas during the dry season. 

Also see Chapter 3, Contaminants and Water 

Quality.

Sacramento County’s National Pollutant 

Discharge Elimination System (NPDES) 

Municipal Permit requires reduction of 

pollutants found in urban stormwater 

runoff to the maximum extent possible. 

Stormwater detention basins are 

constructed as urban expanses east and 

upstream of the Refuge are developed. 

These basins are effective in reducing 

pollutants by 30 percent to 90 percent. The 

pollutants that are not detained will likely 

enter the Refuge in runoff, potentially 

affecting fish and wildlife.
Stone Lakes NWR Comprehensive Conservation Plan 67

Land Use Changes

Urbanization and Vineyard Conversion

Elk Grove incorporated as a city in 2000 

and had the fastest growth rate for any 

large U.S. city between July 2004 and July 

2005 (USDOC 2006). The city adopted its 

general plan in November 2003. When the 

City of Elk Grove incorporated, it adopted 

as a feature of its general plan, the urban 

service boundary previously identified in 

the Sacramento County General Plan, which 

defines the limit of urban development in the 

County. A 90-acre portion of the Wetland 

Preserve Unit of the Refuge lies within 

Elk Grove’s city limit. As provided for in 

the Elk Grove general plan, approximately 

8,000 acres of former agricultural land 

east and upstream of the Refuge is now 

being developed into residences, a regional 

shopping mall and office parks. Over 

18,000 additional homes are expected to 

be constructed by 2010 on land previously 

supporting dry and irrigated pastureland 

and crops (SACOG 2000). Many migratory 

birds which frequent the Refuge are also 

dependent on habitats outside of the Refuge. 

For example, the greater sandhill crane 

has a wintering range of approximately 

three square miles (G. Ivey, pers. comm. 

2003). Therefore, cranes utilizing the 

Refuge also rely on nearby agricultural 

fields, grasslands and wetlands for feeding, 

loafing, etc. As open land is lost, these birds 

are either forced to fly longer distances to 

suitable habitat or pushed into smaller and 

smaller parcels. Over the last ten years, 

the ability of the eastern Sacramento-San 

Joaquin Delta region to support wintering 

cranes and other species such as long-billed 

curlew, white-faced ibis, burrowing owl and 

Swainson’s hawk has declined and continues 

to be threatened by urban development 

and conversion of pasture and row crops to 

vineyards. From 1992 to 2004, the acreage 

planted in vineyards within the approved 

Refuge boundary increased from 685 to 

2,013 acres. The acreage of vineyards in 

Sacramento County nearly doubled from 

1998 to 1999 (Sacramento County 1999, 

Sacramento County 2000). Whereas smaller 

vineyards interspersed with pasture, 

croplands and natural habitats can support 

a variety of wildlife, large expanses of 

vineyards provide little to no habitat for 

migratory birds and other wildlife.

Other Human Impacts

Air Quality

Poor air quality injures wildlife and 

vegetation, causes acidification of water, 

accelerates weathering of buildings and 

other facilities and impairs visibility. Air 

quality, and pollution control in particular, is 

regulated by a number of Federal and State 

agencies. Both the State of California and 

the Federal government have established 

a variety of ambient air quality standards. 

PM10 land ozone are two pollutants that 

are monitored and used to determine air 

quality on a daily basis. PM10 refers to 

particulate matter suspended in the air that 

is smaller than 10 microns, which are small 

enough to reach the lungs. Ozone is the 

main component of photochemical smog, 

which is formed through a series of chemical 

reactions involving compounds known as 

ozone precursors. 

Sacramento County PM10 emissions are 

generated by a variety of sources, primarily 

entrained road dust, construction and 

demolition activities. Farming operations 

and agricultural waste burning are also 

important sources. Motor vehicles are the 

primary contributors to regional ozone 

concentrations because they are sources 

of ozone precursors. The U.S. EPA has 

declared that the Sacramento region is not 

meeting air quality standards. The Federal 

air quality standard for ozone is exceeded 

several times a year and the County has 

been classified as a PM10 nonattainment 

area (USEPA 2006). 

Illegal Activities

The majority of illegal activities involve 

some sort of trespass by people or incursions 

by feral animals, such as cats and dogs. 

Trespass occurs in the form of walking, 

jogging, horseback riding,, hunting, 

fishing, and plant and material collecting. 

Trespassing results in poaching, wildlife 

disturbance, littering, vandalism and 

wildfires. Feral dogs and cats disturb and 

kill native wildlife and disturb cattle used 

to graze managed grasslands. Feral animal 
68 Stone Lakes NWR Comprehensive Conservation Plan

feces can also spread disease to native 

wildlife populations. Noxious weeds are 

spread when people and animals trespass 

into previously uninfested areas. Unwanted 

pets (rabbits, chickens, guinea pigs, dogs, 

cats) that are commonly released at entrances 

to the Refuge can cause similar problems.

Illegal dumping of both non-hazardous and 

hazardous materials (e.g., methamphetamine 

lab waste, pesticides, waste oil) near Refuge 

entrances presents an ongoing concern. 

Littering along Interstate-5, particular 

where commercial truck rigs make overnight 

rest stops (e.g., Hood-Franklin Road exit), 

has also become a significant problem 

as traffic increases on the interstate. 

The Refuge works with the County of 

Sacramento and the California Department 

of Transportation (Caltrans) to remove 

debris as quickly as possible but additional 

efforts and more cooperation are needed. 

Finally, arson-caused or accidental fires 

along Interstate-5 have become a serious 

management concern as the Refuge has 

expanded east of the freeway (i.e., Wetland 

Preserve Unit). As a result, the Refuge 

has pursued new partnership opportunities 

with the Elk Grove Community Services 

District under the Wildland Urban Interface 

program to create adequate firebreaks and 

ensure protection of adjacent communities 

such as the Stonelake subdivision.

More serious crimes, such as burglary and 

abandonment of burning stolen cars at more 

remote Refuge entrances, occur occasionally 

(one to two times per year). Marijuana 

gardens and evidence of other illegal drug 

activities have also been found. Illegal 

hunting and fishing occur most often along 

easy access points, such as roads or from 

private property.

Mosquito Management

In 1993, the Service and the SacramentoYolo Mosquito and Vector Control 

District entered into an MOU regarding 

management of mosquitoes on the Refuge. 

The goal of the MOU is to minimize 

mosquito production and promote the least 

intrusive approaches to control mosquitoes 

on the Refuge. The Refuge coordinates with 

SYMVCD in a variety of ways to minimize 

mosquito breeding habitat. For example, 

the Refuge staff ensure that wetlands are 

designed and water is manipulated in such a 

way to minimize mosquito production. The 

SYMVCD monitors wetlands on the Refuge 

and plants mosquito fish, when necessary, as 

an initial method of control. Alternately, if 

mosquito larvae are detected, Bti (Bacillus 

thuringiensis israeliensis) or B. sphaericus

may be applied.. 

As a result, mosquito larval control activities 

since 1994 have been largely limited to 

localized (less than five acres) applications 

of larvicides and until 2005, and only three 

applications of an adulticides. In 2005, West 

Nile Virus (WNV) arrived and became 

established in Sacramento and Yolo counties, 

triggering more aggressive mosquito 

control. During 2005, the Refuge received 

ultra-low volume (ULV) ground treatments 

of pyrethrin on 18 occasions from September 

28 through October 12. As of July 2006, 

the Refuge has been adulticided six times 

between June 27 and July 21.

Avian Bird Flu

To date, the virulent form of Highly 

Pathogenic Avian Influenza referred to as 

H5N1 has not been detected in either wild 

or domestic birds or in humans in North 

America. In fact, between 1998 and 2004 

more than 12,000 wild bird samples from 

 Illegal dumping of 

both non-hazardous 

and hazardous 

materials inside and 

at the entrance gates 

to the Refuge is an 

obvious problem.

Photo by Tom Harvey, 

USFWS
Stone Lakes NWR Comprehensive Conservation Plan 69

Alaska were analyzed, and no evidence of 

this virus has been discovered, although 

birds migrating from Asia to Alaska could 

potentially carry the H5N1 virus. 

The Service, U.S. Geological Survey 

(USGS), State and partnering academic 

institutions are continuing surveillance of 

wild birds in Alaska for the H5N1 virus. 

The Service is working with an interagency 

group of scientists and public health and 

policy officials to design an intensified 

effort for surveillance and early detection 

of this virus in wild birds. This effort 

will help ensure that the Service is in 

position to support prompt detection and 

response activities and to take appropriate 

measures to conserve bird populations while 

protecting the safety of employees, partners 

and the public. 

The USGS National Wildlife Health Center, 

in consultation with the Centers for Disease 

Control and Prevention, has produced 

Wildlife Health Bulletin 05-03, entitled 

Interim Guidelines for the Protection 

of Persons Handling Wild Birds With 

Reference to Highly Pathogenic Avian 

Influenza H5N1. While reiterating that the 

H5N1 virus has not been detected in North 

America, these guidelines remind us of the 

importance of sensible safety practices. As 

the situation and information with regard to 

the H5N1 virus changes, these guidelines 

may be updated. 
70 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 71

5 Refuge Vision, Goals, and 

Objectives

Vision Statement 

“Stone Lakes National Wildlife Refuge 

belongs to a limited group among the 

over 540 national wildlife refuges that 

protect fish, wildlife, and habitat within an 

urban area. Through collaboration with 

public and private partners, Stone Lakes 

conserves and enhances a range of scarce 

Sacramento-San Joaquin Delta and Central 

Valley habitats and the fish, wildlife, and 

plants they support. It sustains freshwater 

wetlands, wooded riparian corridors, and 

grasslands that facilitate wildlife movement 

and compensate for habitat fragmentation. 

Managed wetlands are of sufficient size to 

maintain abundant wildlife populations. 

Grasslands consist of a sustainable mix of 

native and desirable nonnative species that 

support a variety of grassland-dependent 

species. The Refuge reduces further habitat 

fragmentation and buffers the effects of 

urbanization on agricultural lands and 

adjacent natural areas within the Delta 

region.

The Refuge pursues a land conservation 

program that complements other regional 

efforts and initiatives. Management 

efforts expand and diversify habitats for 

migratory birds and a range of species at 

risk. The Refuge promotes cooperative 

farming opportunities and strives to 

maintain traditional agricultural practices 

in southwestern Sacramento County that 

have proven benefits for migratory birds 

experiencing declines, such as long-billed 

curlews, Swainson’s hawks and sandhill 

cranes. Through cooperation with other 

agencies, conservation organizations, 

neighbors, and other partners, the Refuge 

develops and manages wetlands in a manner 

that reflects historic hydrologic patterns and 

is consistent with local, State, and Federal 

floodplain management goals and programs. 

Stone Lakes was established as a national 

wildlife refuge because of passionate 

support from people who recognized its 

ecological importance and critical role for 

the floodplain of the Beach-Stone Lakes 

basin.. The community sees the Refuge 

as a sanctuary for fish, wildlife and the 

habitats upon which they depend, a site for 

recreation and learning and a natural setting 

that can enrich their lives according to their 

values. Visitors representing the area’s 

diversity enjoy increasing opportunities 

for accessible recreation that harmonizes 

with Refuge conservation efforts, such as 

hunting, fishing, wildlife observation and 

photography. The education community 

looks to the Refuge as a key partner in 

environmental education programming. 

Volunteers from all walks of life find an 

outlet for their interests and talents in a 

responsive and appreciative setting.”

Volunteers from all 

walks of life find 

an outlet for their 

interests and talents 

in a responsive and 

appreciative setting.

Photo by USFWS
72 Stone Lakes NWR Comprehensive Conservation Plan

Goals 

Goals are descriptive, open-ended, and 

often broad statements of desired future 

conditions that convey a purpose but do not 

define measurable outcomes. Goals translate 

Refuge purposes into management direction. 

Each goal is supported by measurable, 

achievable objectives with specific strategies 

needed to accomplish them. Objectives 

are designed to be accomplished within 15 

years. Actual implementation, however, 

may vary as a result of available funding 

or other resource limitations. Figures 6 

and 7, respectively, show summaries of the 

proposed habitat management and visitor 

services plans for Stone Lakes National 

Wildlife Refuge. 

Currently, the Service manages about 30 

percent of the lands within the approved 

Refuge boundary. This CCP presents goals 

and objectives for only those lands that are 

or will soon be managed by the Service. 

The restoration objectives identified in this 

CCP are consistent with the restoration 

goals identified in Chapter 3B-3 of the 1992 

environmental impact statement (EIS) at 

the time of establishment of the approved 

Refuge boundary (USFWS 1992).

Goal 1. Conserve, enhance, restore and 

manage Central Valley wetland, riparian, 

grassland and other native habitats to 

benefit their associated fish, wildlife, 

plants and special status species. 

Objective 1.A. Within 15 years, establish 

a minimum of 65 acres of valley foothill 

riparian and oak woodland habitat with 

a canopy cover of 20-80% and a canopy 

height of 2-10 meters. These newly 

planted habitats will have a complex 

structure with a canopy, subcanopy 

and understory shrub layer that will 

continue to mature beyond the lifetime 

of this CCP. An additional 40 acres of 

understory shrubs and herbaceous cover 

would be established in areas restored 

from 1995-1998. In the restored valley 

riparian habitats, wild grape will often 

cover trees and shrubs and will dominate 

30 to 50 percent of the ground cover along 

with a shrub layer consisting of wild rose, 

California blackberry, blue elderberry, 

poison oak, buttonbush and willows. The 

herbaceous layer will consist of various 

grasses and sedges. Dominant trees 

will include valley oak, cottonwood, 

California sycamore, white alder (Alnus 

rhombifolia), box elder and Oregon ash. 

Rationale: Over 89 percent of the historic 

riparian woodland and 99 percent of oak 

savanna habitat in the Central Valley 

has been lost or converted since EuroAmerican settlement (DFG 2006). Refuge 

riparian habitat restoration efforts to 

date have produced approximately 107 

acres of restored habitat, primarily on the 

Beach Lake Unit. Based on the riparian 

habitat restoration goals defined in the 

EIS (USFWS 1992), the Service intends to 

restore a minimum of 65 acres of additional 

riparian habitat over the next 15 years. 

Expanding riparian zones along lakes, 

sloughs and waterways will benefit a variety 

of species that use these habitats during 

migration, for nesting, feeding and roosting 

habitat. These restored habitats would 

provide breeding and migratory habitat 

for a variety of riparian dependent species 

which have been identified by the Central 

Valley Habitat Joint Venture as species of 

concern (G. Geupel, pers. comm.), including 

the yellow warbler, song sparrow, spotted 

towhee, yellow breasted chat, black headed 

grosbeak and common yellowthroat. Some 

of these species, extirpated locally or in 

severe decline, such as yellow warbler and 

yellow-breasted chat, would also benefit 

from restoration efforts. Understory shrub 

plantings that include elderberry bushes 

would benefit the Federally-listed valley 

elderberry longhorn beetle. Additionally, 

restoring riparian habitat will help achieve 

the conservation action recommendations 

set forth in the Riparian Bird Conservation 

Plan by the California Partners in Flight and 

the Riparian Habitat Joint Venture (RHJV 

2004). 

Strategies:

1. Restore and expand cottonwood 

riparian forest habitat along the south 

arm of North Stone Lake through 

planting and beaver exclusion fencing. 
Stone Lakes NWR Comprehensive Conservation Plan 73

Expand riparian zone

Flood up in fall

for sandhill cranes

and other waterbirds

Drawdown 1 unit

in Aug for shorebirds

Periodically

flood irrigated

pastures

Nov-March

as habitat for

migratory

waterbirds

Flood up in fall

for sandhill cranes

and shorebirds

Manage grazing

to provide foraging

& loafing habitat

for sandhill cranes

Establish native

plant nursery

Maintain/expand

fencing to

exclude cattle

from riparian

zone

Create/enhance

burrowing owl

habitat

Expand & restore

cottonwood forest

Expand riparian zone

Restore upland veg

Open Water

Non-Refuge Lands

Seasonally Flooded

Wetland Restoration

Natural Riparian Expansion

Riparian Restoration

Managed Wetlands

Unmanaged Wetlands & Vernal Pools

Grasslands, Farmlands, & Other

Riparian Forest

Figure 6. Proposed Habitat Management

Stone Lakes

National Wildlife Refuge

0 0.5 1 2

Miles

0 0.5 1 2

Kilometers
To Stockton

Vernal Pool

Guided Tours

Schools & Other Groups

Guided Tours

Sandhill Crane Viewing

Obs Blind

Accessible

by Boat

Trails, Boardwalk & Fishing

1 Car Top Boat Launch

Trails & Boardwalks

Interpretive Shelter & Kiosk

Cultural Resources Displays

Env. Ed Programs & Staging

Jr. Biologist Trail

Car Top Boat Launch

Pre-Registered Persons/Groups

Stone Lakes

National Wildlife Refuge

Figure 7. Proposed Visitor Services Plan

Car-Top Boat Launch

Refuge Headquarters

Parking

Hiking Trails

Photo Blind or Observation Platform

Waterfowl Hunting

Non-Motorized Boating

Boat Fishing

Wetland Restoration

Seasonal Closure

Non-Refuge Lands

Grasslands, Farmlands & Other

Wetlands & Vernal Pools

Riparian Forest

Open Water

0 0.5 1 2

Miles

0 0.5 1 2

Kilometers
Stone Lakes NWR Comprehensive Conservation Plan 75

2. Expand the riparian zone to a range 

of 150 to 400 feet wide along the 

Sacramento Drainage Canal of the 

South Stone Lake and Headquarters 

Units.

3. Restore approximately 20 acres to a 

combination of native trees, shrubs, 

and grasses on the upland areas of the 

Headquarters Unit. 

4. Establish/enhance subcanopy and 

understory in new and established 

riparian habitat areas on the Beach 

Lake and North Stone Lake units.

5. Establish native plant nursery at 

the Headquarters Unit for use in 

restoration projects.

6. Plant early to mid-successional 

vegetation on the western portion 

of the of the South Stone Lake Unit 

(Lewis Investment Co. tract).

7. Assist the Sacramento Regional 

County Sanitation District in 

expanding the valley oak forest 

along lower Morrison Creek on the 

CAMRAY tract of the Beach Lake 

Unit by seeking funding and other 

support for restoration.

8. Allow expansion of riparian habitat 

along existing riparian corridors 

including managed seasonal wetlands. 

9. Identify and map weed infestations, 

track assessments and treatments and 

produce maps and reports that can be 

shared with other interested parties.

10. Intensify control efforts for perennial 

pepperweed in riparian areas using 

a variety of methods including 

pesticides, mowing, and hand-pulling.

11. Cooperate with U.S. Department 

of Agriculture (USDA) and local 

academic institutions to research new 

methods for controlling invasive plants.

12. Measure habitat characteristics (e.g., 

canopy cover, species composition) of 

riparian plantings in areas with a high 

diversity of bird species, as indicated 

by mist netting data collected over the 

past six years on Beach Lake Unit, to 

guide future restoration efforts.

Objective 1.B: Maintain and manage on 

an annual basis 425 acres of riparian and 

oak woodland habitat, consisting of 360 

acres of existing habitat and 65 acres of 

restored habitat (See Objective 1.A). This 

habitat encompasses riparian and oak 

woodland habitat in various successional 

stages comprising a complex structure 

with a canopy, sub-canopy, and understory 

shrub layer (usually impenetrable). 

Restoration would occur through habitat 

manipulations, including control of 

invasive plant species and restoration 

of the sub-canopy and understory shrub 

layer by planting native species. Wild 

grape often covers trees and shrubs and 

dominates the ground cover along with 

a shrub layer consisting of wild rose, 

California blackberry, blue elderberry, 

poison oak, buttonbush and willows. 

The herbaceous layer consists of various 

grasses and sedges. Dominant trees 

include valley oak, cottonwood, California 

sycamore, white alder, box elder and 

Oregon ash. 

Rationale: Valley foothill riparian habitats 

occur in the Central Valley and the lower 

foothills of the Sierra Nevada and Coast 

Ranges and are associated with low velocity 

flows, floodplains and gentle topography. 

Over 89 percent of the historic riparian 

woodland and 99 percent of oak savanna 

habitat in the Central Valley has been 

lost or converted since Euro-American 

settlement (DFG 2006). These habitats 

comprise a complex structure with a canopy, 

subcanopy and understory shrub layer. 

Based on the population trends and life 

history requirements of various species 

in the Central Valley, the Central Valley 

Habitat Joint Venture has developed a list 

of focal migratory bird species that can be 

used to guide restoration and management 

efforts. Riparian habitats provide breeding 

and migratory habitat for the following focal 

species for the Central Valley, as defined by 

the Central Valley Habitat Joint Venture (G. 

Geupel, PRBO, pers. comm.): yellow warbler, 

song sparrow, spotted towhee, yellow 

breasted chat, black headed grosbeak and 

common yellowthroat. Furthermore, these 

riparian areas support heron and egret 

rookeries that vary in size from ten to 50 

nests. The bird species previously listed and 

others, use a variety of successional stages 
76 Stone Lakes NWR Comprehensive Conservation Plan

within riparian habitat. Maintaining and 

managing high quality riparian habitat, in 

various successional stages, will help achieve 

the conservation action recommendations 

set forth in the Riparian Bird Conservation 

Plan (RHJV 2004).

Strategies:

1. Monitor riparian and oak woodland 

habitats each spring for invasive 

species such as perennial pepperweed 

and yellow star thistle and implement 

control methods based on integrated 

pest management techniques, 

including herbicide applications and 

grazing (see Objective 1.A).

2. Monitor riparian areas for existing 

and newly-established heron and egret 

rookeries (See Strategy 2.B.2). 

3. Maintain and expand fencing along SP 

Cut on the North Stone Lake Unit to 

exclude cattle from riparian areas.

4. Conduct annual surveys of riparian 

habitats for damage by beavers, 

research methods to discourage 

beavers, and implement protection 

measures (e.g., wrapping trees with 

hog wire or fencing).

Objective 1.C: Within five years, enhance 

and maintain approximately 50 acres 

of seasonal and permanent wetlands 

created on the 70 acre of the South Stone 

Lake Unit (Lewis Investment Co. tract) 

by promoting growth of wetland species 

such as swamp timothy, smartweeds, 

watergrass and associated invertebrates. 

These wetland species provide food for 

waterfowl and other waterbirds.

Rationale: Approximately 95 percent of 

wetlands in the Central Valley have been 

lost or converted to other land uses (DFG 

2006). Improving water management on the 

South Stone Lake Unit would reverse some 

of these losses and benefit a wide variety of 

migratory birds and other wildlife, including 

special status species, such as giant garter 

snake, western pond turtle, white-faced ibis, 

greater sandhill crane, long-billed curlew, 

black-bellied plover, black-necked stilt 

and long-billed dowitcher (Limnodromus 

scolopaceus) and help achieve CVJV goals.

Strategies: 

1. Modify existing water delivery system 

on the South Stone Lake Unit to 

deliver water to the Lewis Investment 

Co. Tract.

2. Control undesirable vegetation 

using a combinations of the following 

treatments: mowing, discing, burning, 

herbicide applications and summer 

flooding. 

3. Explore the possibility of applying 

reverse-cycle water management 

on an experimental basis to benefit 

shorebirds. 

Objective 1.D: Manage on an annual 

basis 529 acres as moist soil habitat, 

characterized by a plant composition 

of 50 percent or more moist soil, highenergy waterfowl plant foods including: 

watergrass, swamp timothy and 

smartweeds. Flood approximately 60 

percent of the moist soil units to a depth 

of 2 to 10 inches for dabbling ducks and 

shorebirds and 40 percent to depths of 6 

inches to 3 feet for diving ducks, grebes, 

cormorants, pelicans, waders and other 

waterbirds.

Rationale: All managed seasonal 

wetlands on the Refuge consist of moist 

soil impoundments which support a wide 

variety of waterbirds, with peak numbers of 

waterfowl and shorebirds occurring in the 

late fall and winter. Species groups having 

varying requirements for vegetation and 

water depth. For example, dabbling ducks, 

such as cinnamon and green winged teal, 

mallard and northern pintail prefer to feed 

in shallow water, with an equal ratio of open 

water and emergent vegetation, whereas 

diving ducks, such as bufflehead (Bucephala 

albeola), canvasback and common goldeneye 

(Bucephala clangula) prefer deeper water. 

Shorebirds, such as long-billed dowitcher, 

black-bellied plover, and black-necked 

stilts, feed on mudflats or in shallow water 

of varying depths, depending on species. 

Managed seasonal wetlands on the Refuge 

are currently operated under a fallmigration-oriented regime with flood-up 
Stone Lakes NWR Comprehensive Conservation Plan 77

from mid-September or October through 

May, which optimizes habitat availability for 

fall migrants. Flooding seasonal wetlands 

under a reverse-cycle regime from March 

through August could provide late winter 

food before migration and habitat for 

breeding shorebirds and waterfowl broods. 

Species supported by this objective include 

special status species such as white-faced 

ibis and greater sandhill crane. 

Strategies:

1. Flood moist soil wetland 

impoundments, depending on water 

availability, on Beach Lake and South 

Stone Lake units starting September 1 

and no later than mid-September and 

maintain through March to May for 

migratory and wintering waterbirds, 

including waterfowl, shorebirds and 

sandhill cranes.

2. Stagger the timing of drawdown for 

moist soil units beginning in March.

3. Irrigate units one or two times from 

May through August to promote 

waterfowl food such as watergrass and 

swamp timothy

4. Disc and/or mow 25-50 percent of the 

units to stimulate growth of waterfowl 

food plants and mow or disc to 

maintain an equal ratio of open water 

to emergent vegetation.

5. Control undesirable plants such as 

cocklebur and joint grass using one 

or more of the following treatments: 

mowing, discing, burning, herbicide 

applications, or summer flooding.

6. Explore the possibility of applying 

reverse-cycle water management 

on an experimental basis to benefit 

shorebirds.

7. Draw down one permanent wetland 

unit beginning in August to provide 

habitat for migrating shorebirds. 

Flood the unit again in late September, 

when other wetlands are being flooded.

Objective 1.E: Maintain 452 acres 

annually of unmanaged seasonal wetlands 

(i.e., wetlands with no capability to 

manipulate water regimes) so they 

support 50 percent or more moist soil, high 

energy waterfowl plant foods, including 

watergrass, swamp timothy, and 

smartweeds, interspersed with open water 

while controlling undesirable vegetation, 

such as cocklebur, yellow star thistle and 

perennial pepperweed to benefit wintering 

and migratory waterfowl, as well as other 

wetland-dependent species. 

Rationale: Unmanaged seasonal wetlands 

with no capability for water manipulations 

are found on all units of the Refuge. These 

wetlands receive water passively from rain 

and runoff only and are typically dry during 

summer. Once flooded, these wetlands 

attract a variety of waterbirds such as 

cinnamon teal, northern pintail, whitefronted goose, black-bellied plover, black 

necked stilt, long-billed dowitcher, sandhill 

crane and long-billed curlew. 

Strategies:

1. Monitor unmanaged wetlands each 

spring for undesirable vegetation 

such as cocklebur and other noxious 

weeds such as yellow star thistle and 

perennial pepperweed and implement 

control methods as needed. 

2. Use burning, grazing, discing, mowing 

and/or herbicide application to control 

the growth of invasive species and 

promote the growth of desirable 

wetland plants, such as watergrass, 

swamp timothy, smartweeds and 

nutsedges, in seasonal swales.

Objective 1.F: Annually maintain 136 

acres of vernal pool seasonal wetlands 

characterized by greater than 70 percent 

native vernal pool vegetation. 

Rationale: Vernal pool habitats support 

a variety of vernal pool species, including 

the federally endangered vernal pool fairy 

shrimp and vernal pool tadpole shrimp, as 

well as various species of special concern, 

including vernal pool plant species (USFWS 

2006). These pools are best managed 

through prescribed grazing from November 

through June. Without grazing, a dense 

layer of nonnative annual grasses can 

exclude native vernal pool plants and 

consume water to the extent that vernal 

pools become prematurely dry. Grazing 

reduces the competitiveness of native plants 

versus nonnative plants, and may prolong 

inundation of vernal pools in the spring (J. 
78 Stone Lakes NWR Comprehensive Conservation Plan

Marty, TNC, pers. comm.).

Strategies:

1. Monitor wetlands each spring for 

undesirable vegetation, such as 

cocklebur, and noxious weeds, such 

as yellow starthistle and perennial 

pepperweed and implement control 

efforts as needed. 

2. In cooperation with the landowner, 

develop a grazing management plan 

for the Wetland Preserve Unit that 

maintains a residual dry matter 

level, as measured in August through 

September, of 800-1000 lbs/acre.

3. Depending on air quality regulatory 

restrictions, employ prescribed burns 

to reduce nonnative annual grasses 

and replicate the historical fire regime 

as closely as possible.

4. Develop proposals and support 

research to characterize plant and 

animal communities in natural versus 

created vernal pools.

Objective 1.G: Annually maintain 715 

acres of deep water wetlands (including 

wetlands with and without a capability 

to manipulate water regimes), lakes, 

sloughs and SP Cut to provide breeding, 

foraging and loafing habitat for waterfowl 

and other wetland dependent species, 

such as giant garter snakes and western 

pond turtles. Deep water wetlands will 

be characterized by water depths of 

greater than three feet supporting wetland 

plants species such as tules, cattails, 

burreed (Sparganium spp.) and water 

primrose. Wetlands with the capability to 

manipulate water regimes (106 acres) will 

be managed to support a 50:50 ratio of tall 

emergent vegetation to open water. 

Rationale: Permanent wetlands include 

wetlands, lakes, sloughs and waterways with 

different water management capabilities. 

Deeper water habitats interspersed with tall 

emergent vegetation, such as cattails and 

tules, provide excellent habitat for a variety 

of migrating, wintering and resident birds, 

including special status species, such as 

greater white-fronted geese, canvasbacks, 

northern pintails, wood ducks, common 

moorhens, American bitterns, American 

white pelicans and pied-billed grebes. An 

approximately equal percentage of open 

water for foraging and tall emergent 

vegetation for cover provides an optimal 

mix of habitat types. Riparian habitats 

associated with these wetlands may support 

colonies of nesting great blue herons, great 

egrets, double-crested cormorants, blackcrowned night herons, and snowy egrets and 

a variety of raptors such as the Swainson’s 

hawk. Fallen trees and logs provide basking 

sites for species such as western pond 

turtles and permanent wetlands, sloughs 

and waterways provide habitat for the 

endangered giant garter snake. Many of 

these wetlands were degraded through 

dredging, farming and other activities 

and are currently further threatened by 

degradation of water quality and invasive 

aquatic weeds such as water hyacinth.

Strategies:

1. Reduce human disturbances to nesting 

birds and other wildlife on deep water 

habitats such as lakes, sloughs and the 

SP Cut by limiting public access.

2. Continue to work in partnership with 

private landowners and local and State 

agencies and academic institutions to 

control water hyacinth and participate 

in the Stone Lakes Basin Water 

Hyacinth Control Program.

3. Within five years, survey aquatic 

plants in South Stone Lake and map 

distribution of Brazilian elodea and 

other non native plants to determine 

if control efforts are needed and if so, 

what methods can be used .

4. Cooperate with the U.S. Department 

of Agriculture and local academic 

institutions on evaluating alternate, 

nonchemical methods of controlling 

invasive weeds.

5. Assess necessity and feasibility of 

drawing down North Stone Lake to 

solidify a portion of the bottom of the 

lake to stimulate plant growth.

6. Maintain approximately an equal ratio 

of emergent vegetation to open water 

on the Beach Lake and South Stone 

Lake units through a combination 
Stone Lakes NWR Comprehensive Conservation Plan 79

of drawdowns, mowing, discing and 

prescribed burning in sloughs. 

7. Drawdown managed permanent 

wetlands every two to four years to 

control carp populations and improve 

germination of desirable wetland 

plants.. 

8. Maintain sanctuary areas for nesting 

waterbirds, (e.g., pied-billed grebes) 

waterfowl broods, giant garter snakes, 

and western pond turtle from May 

through September in the central 

portion of South Stone Lake (see 

Figure 6).

Objective 1.H: Manage and enhance 

approximately 1,900 acres of non-irrigated 

grasslands on the North Stone Lake Unit 

on an annual basis to provide a variety of 

grass heights and densities as measured 

by residual dry matter (RDM) at the end 

of the grazing season, which is typically 

November to June depending primarily on 

precipitation and other factors. Pasture 

rotation reduces grazing pressure on 

different pasture units and promotes a 

diversity of grassland-dependent species, 

such as arctic nesting geese, shorebirds, 

songbirds, burrowing owl and other 

raptors, sandhill crane and long-billed 

curlew which have been identified by the 

Service as focal species.

Rationale: Over 99.9 percent of historic 

native grasslands in the Central Valley have 

been lost to agricultural conversion and 

urban development since Euro-American 

settlement (DFG 2006). The large ungulates, 

pronghorn antelope and tule elk, that once 

grazed these grasslands were extirpated 

from the valley by the 1870s. The natural 

hydrologic regime of the area has also 

been irreversibly modified. Despite these 

changes, the 2,600-acre North Stone Lake 

Unit is one of the largest and relatively 

unaltered grassland areas left in the Stone 

Lakes Basin. It supports a variety of special 

status species, such as the greater sandhill 

crane, burrowing owl, Swainson’s hawk, 

California horned lark, long-billed curlew 

and western meadowlark. Since grazing was 

reintroduced following a ten-year absence, 

many of the species mentioned above 

expanded their use of the Refuge. 

Strategies:

1. Graze cattle on the North Stone Lake 

Unit from November 1 to July 15; 

actual termination dates will vary from 

year to year depending on rainfall and 

grass production.

2. Use integrated pest management 

techniques, including prescribed 

fire, mowing, discing, hand removal 

and herbicide applications, to reduce 

invasive plants, such as yellow 

starthistle, pepperweed and other 

undesirable grassland vegetation.

3. Implement a long term grazing 

management plan developed in 

collaboration with USDA Natural 

Resource Conservation Service 

(NRCS) and other range management 

experts. The plan prescribes 

stocking rates to achieve varying 

grass heights and densities in the five 

pastures of the unit to accommodate 

habitat requirements of breeding 

and wintering bird species, including 

sandhill cranes, long-billed curlews 

and western meadowlarks. The overall 

goal is to annually rotate grazing 

pressure (e.g., low, medium or high) 

among the five pastures, resulting in a 

range of grass heights and densities. 

Two pastures will be maintained with 

relatively lower residual dry matter 

(RDM) values as measured at the end 

of the grazing season (1,200 lbs/acre), 

two pastures with medium RDM 

values (1,750 lbs/acre) and one pasture 

with a higher RDM value (+2,500 lbs/

acre). . 

4. Enhance and create habitat for 

burrowing owls by reintroducing 

ground squirrels to the North 

Stone Lake Unit and constructing 

and maintaining artificial burrows 

until sufficient natural burrows are 

available.

5. Develop long term monitoring plan to 

survey population trends of greater 

sandhill cranes, arctic nesting geese, 
80 Stone Lakes NWR Comprehensive Conservation Plan

long-billed curlews, white-faced 

ibis, burrowing owls, and western 

meadowlarks to evaluate wildlife 

responses to range management.

6. Develop methodologies to conserve, 

enhance and restore native grasses on 

the North Stone Lakes Unit through 

test plots in conjunction with USDA 

NRCS and Agriculture Plant Material 

Center.

Objective 1.I: Annually maintain 460 

acres of irrigated pasture/wet meadow to 

provide habitat for a variety of grassland 

dependent species, including sandhill 

cranes, white faced ibis, long-billed curlew 

and arctic nesting geese. 

Rationale: With less than one percent of 

native grasslands left in the Central Valley, 

many grassland dependent species now rely 

on dry and irrigated pastures for migrating 

and wintering habitat. Irrigated pastures 

on the North Stone Lake Unit support the 

largest concentration of native grasses on 

the Refuge. Irrigated pasture is sheetflooded in winter to bring invertebrates to 

the surface, providing foraging habitat for 

cranes and shorebirds.

Strategies:

1. Continue irrigation of 460 acres of 

pastures on the North Stone Lake 

and South Stone Lake units and the 

Gallagher tract from June through 

October.

2. If feasible, sheet flood irrigated 

pastures to a depth of less than 

six inches every two weeks from 

November through March on the 

North Stone Lake Unit (also see 

2.A.2).

3. Provide short grass habitat through a 

managed grazing program from July 

through October.

4. Develop a monitoring plan to survey 

native grasses and develop mapping 

capabilities and strategies to expand 

native grasses.

Objective 1.J: Restore approximately 30 

acres to grassland habitat consisting of 

a minimum of 70 percent native grasses 

including; needlegrass, bluegrass (Poa 

spp.), rye grass, Elymus spp., and Melica 

spp. on various Refuge units within 10 

years to promote biodiversity and improve 

the grassland communities on the Refuge.

Rationale: Native grasses once covered 

nearly 22 million acres of California, 

including much of the Central Valley (Heady 

1977). Today, over 99.9 percent of these 

grasslands have been lost (DFG 2006). 

Although little is known about the original 

composition of native grasses of the Stone 

Lakes Basin, purple needlegrass may have 

dominated the valley grasslands with a 

mix of other perennial grasses, including 

bluegrass, rye grass, Elymus spp. and 

Mellica spp.; annual grasses such as Fescue 

(Festuca spp.); and a mixture of broadleaved forbs (Heady 1977; Stebbins 1965). 

Because little is known about the original 

composition of the grasses and dramatic 

changes in land use and hydrology have 

occurred, local experts are the best source of 

information when planning native grassland 

restorations.

Strategies:

1. Establish small (less than 0.25 acre) 

experimental native grass plots before 

large scale restoration activities are 

conducted.

2. Remove nonnative seed sources by 

mowing, discing, burning, or chemical 

applications for two seasons before 

establishing native grasses and control 

broadleaves and other invasive plants 

on newly restored areas for three 

years or more.

3. Maintain grasslands by periodic 

disturbance, such as mowing, grazing, 

burning, or discing outside of the 

breeding season for birds.

4. Use local expertise in developing 

native grassland restoration plans.

5. Restore 3-5 acres of the western 

portion of the South Stone Lake Unit 

to a grassland community with an 

objective of 60 percent native grasses 

through discing, seeding, mowing and 

herbicide applications outside of the 

breeding season for birds.
Stone Lakes NWR Comprehensive Conservation Plan 81

6. Develop a monitoring plan to assess 

the success of native grass restoration 

projects.

Objective 1.K: Within 15 years, coordinate 

the Refuge land conservation program to 

protect 75 percent of the land within the 

approved Refuge boundary to help achieve 

the Central Valley Joint Venture (CVJV) 

regional habitat protection goals. 

Rationale: One of the goals identified 

in the EIS that established the approved 

Refuge boundary (USFWS 1992), is 

creating linkages between Refuge 

habitats and habitats on adjacent lands 

to reverse the impacts of past habitat 

fragmentation on wildlife and plants. 

Therefore, priority should be given to 

conserving lands within the approved 

Refuge boundary and coordinating Refuge 

land conservation activities with other 

nearby regional conservation projects 

to compensate for habitat fragmentation 

caused by agricultural conversion and urban 

development. The CVJV is a partnership 

of conservation organizations and State 

and Federal agencies whose mission is 

to work collaboratively through diverse 

partnerships to protect, restore and 

enhance wetlands and associated habitats 

for waterfowl, shorebirds, waterbirds and 

riparian songbirds, in accordance with 

conservation actions identified in the CVJV 

Implementation Plan. Through these 

actions, the CVJV aims to advance its vision 

of providing diverse habitats necessary 

to sustain migratory bird populations in 

perpetuity for the benefit of those species, 

resident wildlife and the public. The 

Central Valley of California is the most 

important waterfowl wintering area in the 

Pacific Flyway, supporting 60 percent of 

the total duck and goose population. In 

its implementation plan, the CVJV sets 

out habitat protection, enhancement and 

restoration objectives for sub-basin of the 

Central Valley, including the Sacramento 

San Joaquin Delta.

Strategies:

1. Coordinate Refuge land conservation 

activities with local and State agencies 

and private organizations, including 

the Sacramento Regional County 

Sanitation District, Sacramento 

County Department of Regional Parks, 

Recreation and Open Space, California 

Department of Parks and Recreation, 

California Department of Water 

Resources, The Nature Conservancy, 

the Trust for Public Land and the 

American Land Conservancy.

2. Continue to seek congressionallyappropriated funds (including Land 

and Water Conservation Funds and 

Migratory Bird Conservation Funds) 

and other Federal, State and private 

funding for land conservation.

3. Acquire agricultural and conservation 

easements on farmland and other 

fish and wildlife habitats within the 

approved Refuge boundary.

4. Participate actively in regional land 

planning efforts by Sacramento 

County, Cities of Elk Grove and 

Sacramento, Sacramento Area Council 

of Governments, and others that may 

promote the maintenance of open 

space and wildlife corridors between 

the Refuge and other regional open 

space areas. 

5. Within one year, complete conveyance 

of fee title interest in the 150-

acre Beach Lake Mitigation Bank 

(Beach Lake Unit) from California 

Department of Transportation.

6. Within two years, finalize a cooperative 

agreement with the Sacramento 

Regional County Sanitation District 

for joint management of the 1,800 

acres of the Sacramento Regional 

Wastewater Treatment Plant 

Bufferlands lying within the approved 

Refuge boundary.

7. Within 15 years, secure funding to 

protect 75 percent of land with the 

approved Refuge boundary by working 

with willing landowners.

Objective 1.L: Coordinate Refuge 

habitat conservation efforts with other 

private and public conservation efforts 

within the Sacramento-San Joaquin 

Delta to contribute to regional habitat 

conservation needs.
82 Stone Lakes NWR Comprehensive Conservation Plan

Rationale: The EIS establishing the 

approved Refuge boundary (USFWS 1992) 

identified two goals: (1) coordinate Refuge 

land acquisition and management activities 

with other agencies and organizations 

to maximize the effectiveness of Refuge 

contributions to regional habitat needs, and 

(2) preserve, enhance, and restore Central 

Valley wetlands and agricultural lands to 

provide foraging and sanctuary habitat 

to achieve distribution and population 

levels of migratory waterbirds consistent 

with goals and objectives of the Central 

Valley Joint Venture (CVJV). Therefore, 

coordination of the conservation efforts of 

various management entities should support 

a greater diversity of fish and wildlife values 

and recreational opportunities. Under the 

North American Waterfowl Management 

Plan, the CVJV was established for habitat 

conservation and management of migratory 

waterbirds in the Central Valley. Current 

CVJV habitat objectives for the SacramentoSan Joaquin Delta to which the Refuge 

may contribute include: (1) restore 19,000 

acres of wetlands; (2) enhance 2,112 acres 

of wetlands; and (3) enhance 23,000 acres 

of agricultural land. The Service would 

coordinate efforts with ongoing private 

and public conservation projects, including 

the CVJV, Riparian Habitat Joint Venture, 

Cosumnes River Preserve, Yolo Basin 

Wildlife Area, Delta Meadows State Park 

and other State-owned Delta properties.

Strategies:

1. Within three years, modify the 

existing cooperative agreement with 

Sacramento County Department of 

Regional Parks, Recreation and Open 

Space for their 1,567-acre portion of 

the North Stone Lake Unit so the 

agreement has a 30-year duration, and 

includes the habitat and visitor use 

strategies outlined in the CCP and 

Sacramento County’s revised Draft 

North Stone Lake Management and 

Restoration Plan. 

2. Within three years, secure long term 

management through cooperative 

agreement of the California 

Department of Parks and Recreation 

1,224-acre portion of the North Stone 

Lake Unit.

3. Within five years, develop a 

cooperative agreement with California 

Department of Water Resources for 

joint management of the 410 acres 

they own within the approved Refuge 

boundary.

4. Pursue inclusion of the Service as 

a signatory to the joint operating 

agreement for the Cosumnes River 

Preserve to support the conservation 

and management of lands within and 

adjacent to the approved Refuge 

boundary. 

5. In cooperation with the Natural 

Resources Conservation Service 

(NRCS) and other agencies and 

private organizations, pursue 

enhancement of privately-owned lands 

within and outside of the approved 

Refuge boundary by working with 

landowners through various programs, 

such as Partners for Fish and 

Wildlife and NRCS programs (e.g., 

Conservation Reserve Enhancement 

Program, Environmental Quality 

Incentives Program, and Wildlife 

Habitat Incentives Program).

6. Continue to participate actively in 

regional land use planning by State, 

county and municipal entities that may 

affect Refuge resources or complement 

Refuge conservation goals (see also 

1.M).

Objective 1.M: Manage Refuge floodplain 

lands in a manner consistent with local, 

State and Federal flood management, 

sediment and erosion control and water 

quality objectives as described in the 

environmental impact statement (EIS) 

establishing the approved Refuge 

boundary.

Rationale: The importance of the BeachStone Lakes Basin as a flood storage area 

during winter high flow events continues to 

increase with upstream urban development. 

The resulting changes in the flooding 

regime have also reduced the viability of 

some agricultural operations and modified 

patterns of remaining natural vegetation. 
Stone Lakes NWR Comprehensive Conservation Plan 83

In the EIS that established the approved 

Refuge boundary (USFWS 1992), the 

Service recognized flood storage as an 

important benefit and natural component 

of the Beach Stone Lakes ecosystem. 

Refuge restoration and management will be 

consistent with Federal, State and local flood 

guidelines.

Strategies:

1. Participate in regional interagency 

floodplain management planning 

efforts that may affect the BeachStone Lakes Basin, including the 

North Delta Improvement Group, 

Lower Morrison Creek planning, 

Mokelumne-Cosumnes Watershed 

Alliance, Pt. Pleasant Flood Control 

Working Group and Sacramento River 

Planning Forum.

2. Implement Refuge habitat 

improvement strategies so that they 

do not exacerbate local or regional 

flooding, degrade water quality, or 

cause erosion impacts for adjacent or 

nearby landowners or residents.

3. Review and participate in regional 

planning activities sponsored by 

Sacramento County and local 

municipalities, such as the City of 

Elk Grove, which may affect flooding 

regimes or water quality in the BeachStone Lakes Basin. 

4. Develop a Refuge levee flood control 

channel maintenance MOU in 

coordination with local agencies, 

such as reclamation and resource 

conservation districts, the City of Elk 

Grove, and Sacramento County, that is 

consistent with existing or future flood 

control policies.

Objective 1.N: Within 10 years of CCP 

approval, work toward achieving the 

water quality supply standard for 

wetlands and fish and wildlife resources 

set forth by the U.S. Environmental 

Protection Agency (USEPA), the 

California Department of Fish and Game 

(DFG) and the Regional Water Quality 

Control Board.

Rationale: Establishing a water quality 

monitoring program was recommended as a 

mitigation measure in the EIS establishing 

the approved Refuge boundary (USFWS 

1992) and as part of subsequent water 

quality investigations (Thomas 2003). A 

water quality monitoring program can be 

used to further education and outreach 

efforts to local landowners, businesses 

and agricultural landowners, and can 

inform regulatory activity, if needed. 

Current threats to Refuge water quality 

include: eutrophic conditions (excess 

nutrients), turbidity, low dissolved oxygen, 

contaminants in urban and agricultural 

runoff (e.g., polycyclic aromatic 

hydrocarbons (PAHs), fecal coliform and 

pesticides) as well as mercury from historic 

mining operations.

Two options exist for the Refuge to comply 

with the Central Valley Regional Water 

Quality Control Board’s (Regional Board) 

Irrigated Lands Conditional Waiver for 

water dischargers: filing as an individual 

discharger; or joining a discharge Coalition 

Group. Discharges from the Refuge into 

Waters of the State are not a regular 

occurrence and only occur periodically 

during flood events in which most of the 

flood water stays on Refuge lands and is 

not discharged. In addition the Refuge 

cooperates with the SRCSD Bufferlands 

staff to collect and analyze water samples 

to assess any impacts resulting from the 

application of aquatic herbicides. The 

Refuge complied with water quality testing, 

to assess any concentration of aquatic 

herbicides, in compliance with the California 

Department of Boating and Waterways 

National Pollution Discharge Elimination 

System (NPDES) permit. Given that 

minimal discharge, if any, occurs from the 

Refuge and that water quality monitoring 

is already occurring, the Refuge will file as 

an individual discharger, or as a Coalition 

Group Member if appropriate.

To comply with the Irrigated Lands 

Conditional Waiver as an Individual 

discharger, the Refuge must file a Notice 

of Intent (NOI) to comply and a Farm 

Evaluation Report. Additional required 

reports will include a Monitoring and Report 

Program Plan and water quality monitoring, 
84 Stone Lakes NWR Comprehensive Conservation Plan

evaluated in a complete annual report to 

the Regional Water Board. In addition, 

technical reports may also be required, by 

the Regional Board, should water quality 

problems occur. The requirements for those 

that join a Coalition Group and file under the 

Conditional Waiver for Coalition Groups are 

identical except that a Watershed Evaluation 

Report is required in place of a Farm 

Evaluation Report. The reports required 

from the Coalition Groups include the filing 

of a NOI and General Report, Monitoring 

and Reporting Program Plan, Annual 

Monitoring Reports and the potential for 

a development of a Management Plan if 

required to resolve exceedance of water 

quality objectives.

Strategies:

1. Work to ensure coverage under 

the Central Valley Regional Water 

Quality Control Board Irrigated 

Lands Conditional Waiver, either as an 

Individual discharger or as a Coalition 

Group member if appropriate.

2. Develop a Refuge water quality 

monitoring program to track changes 

in contaminant concentrations, and 

water quality parameters (pH and 

dissolved oxygen) resulting from 

current and future land use patterns 

around the Refuge within five years. 

3. Develop a long-term water quality 

monitoring program to assess the 

effects of non-point sources of pollution 

(including stormwater and agriculture 

runoff) entering the Refuge and the 

contaminant levels in fish and other 

biota.

4. Develop strategies to work with 

local landowners, businesses and 

neighborhood organizations within 

the watershed to educate and reduce 

quantities of pesticides and runoff 

entering the Refuge.

5. Expand the Refuge outreach and 

education effort to inform upstream 

urban residents and businesses of the 

sensitivity of downstream water uses. 

6. Develop a partnership with Franklin 

High School to monitor water quality 

on the Refuge.

Goal 2. Conserve, enhance, and restore 

high quality migrating, wintering and 

breeding habitat for migratory birds within 

the Sacramento San Joaquin Delta of the 

Central Valley.

Objective 2.A: Manage 2,950 acres of 

Refuge lands and cooperate with nearby 

farmers and landowners to conserve and 

enhance agricultural lands and habitats 

that support 400-700 greater and lesser 

sandhill cranes wintering in the Stone 

Lakes Basin. The Refuge will continue 

management of seasonal wetlands and 

irrigated pasture to provide roosting and 

foraging habitat and pursuing projects 

and partnerships to maintain dry and 

irrigated pastures, wheat, corn, and 

alfalfa for cranes foraging in the basin.

Rationale: The greater sandhill crane 

is listed by the State as a threatened 

subspecies, under the California 

Endangered Species Act (CESA). Cranes 

winter in the Central Valley and depend 

on a combination of agricultural lands, 

wetlands and pasture. As urban expansion 

and conversion of agricultural crops and 

pastures to vineyards continues, habitat 

availability for cranes has decreased. 

Winter home ranges for greater sandhill 

cranes are relatively small, averaging less 

than one square mile, despite fluctuating 

food availability during the winter season 

(G. Ivey, pers. comm.). Nightly roost sites 

need to be in close proximity (less than one 

mile) to feeding sites. The Refuge can play 

an important role in the recovery of this 

subspecies by providing winter roosting and 

foraging habitat to support approximately 

200 to 300 greater sandhill cranes near the 

North and South Stone Lake units and the 

surrounding area. 

Strategies: 

1. Begin flood up of seasonal and 

permanent wetlands on the Beach 

Lake and South Stone Lake units in 

early September to provide habitat 

for arriving (migrating) cranes, 

particularly when roosting habitat in 

the area is in short supply.

2. Periodically sheet-flood irrigated 

pastures in winter to provide foraging 
Stone Lakes NWR Comprehensive Conservation Plan 85

opportunities on the North Stone Lake 

Unit.

3. Continue grazing the North Stone 

Lake Unit to provide foraging and 

loafing habitat adjacent to roosting 

sites in wetlands (see objective 1.F).

4. Develop and host workshops to 

provide private landowners with 

information about USDA, NRCS and 

other Federal, State and private grant 

and incentive programs aimed at 

maintaining small grain fields for crane 

forage and protecting or enhancing 

other habitats important for wintering 

crane within a five-mile radius of the 

Refuge.

5. Maintain 40 to 60 acres of agriculture 

fields on the Headquarters Unit of the 

Refuge for foraging cranes. Crops 

could include corn, winter wheat and 

other small grains.

6. Conduct bimonthly sandhill crane 

surveys and coordinate results with 

appropriate researchers and refuges 

including the Cosumnes River 

Preserve and Modoc and Malheur 

national wildlife refuges. 

7. Incorporate crane roosting habitat 

characteristics (e.g., shallow water, 

small islands with gravel, and 

minimizing human disturbance) into 

any new wetland development plans.

Objective 2.B: Develop monitoring 

strategies for focal species identified in 

various regional bird conservation plans 

to assess current and guide future habitat 

restoration activities. The regional plans 

include: the Central Valley Joint Venture 

Implementation Plan, the Riparian Bird 

Conservation Plan, the Grassland Bird 

Conservation Plan, the Oak Woodland 

Bird Conservation Plan, the North 

American Waterbird Conservation 

Plan, the North American Waterfowl 

Management Plan, and the North 

American Landbird Conservation Plan.

Rationale: Population monitoring and 

research assessing the habitat requirements 

of migratory birds is needed to evaluate 

the effectiveness of Refuge management 

strategies and facilitate adaptive 

management. Monitoring and research on 

the Refuge, in cooperation with other similar 

efforts in the Central Valley, will provide 

valuable information about population trends 

and assist with development of overall 

strategies for the recovery and management 

of migratory birds and other key species 

groups. Collaborative efforts between 

the Refuge and other agencies, academic 

institutions, and private organizations will 

increase the effectiveness of data collection 

efforts, expand the resources available and 

enable the Service to address a larger array 

of research and monitoring needs. 

The Sacramento-Yolo Mosquito and Vector 

Control District (SYMVCD) has monitored 

landbirds on the Refuge weekly through 

mist netting and banding since 1995. The 

program has assisted the Service with 

assessing the quality of Refuge riparian 

habitats and avian species diversity. The 

goals of this program are to: assess the role 

of wild birds as reservoirs for mosquitoborne diseases such as Western Equine 

Encephalitis, St. Louis Encephalitis, and 

West Nile virus; assess the usefulness 

of bird populations as an early warning 

system for potential viral episodes; and 

provide information regarding species 

diversity, population status, seasonal use and 

reproductive success and recruitment on the 

Refuge.

Strategies:

1. Conduct biweekly waterfowl, 

shorebird and waterbird censuses 

from September through June and 

coordinate surveys with the annual 

inter-agency mid-winter waterfowl 

survey.

2. Continue monitoring of existing heron 

and egret rookeries and annually 

survey suitable riparian areas for new 

colonies (See Strategy 1.B.2).

3. Pursue opportunities to recruit 

qualified volunteers and develop 
86 Stone Lakes NWR Comprehensive Conservation Plan

partnerships with resource agencies, 

academic institutions and private 

organizations to accomplish monitoring 

and research projects related to 

Refuge habitats and wildlife.

4. Develop and annually update a list 

of Refuge monitoring needs with 

universities in the region and other 

agencies which conduct research.

5. Develop surveys on the South Stone 

Lake, Headquarters, and Wetland 

Preserve Units and other lands as they 

come under Refuge management.

6. Develop data management strategies 

to store data and make data available 

to other researchers.

7. Assess feasibility of creating tricolored 

blackbird habitat in grassland habitat 

(e.g., planting large California 

blackberry patches and expanding tule 

areas in wetlands for nesting).

Goal 3. Provide visitors with wildlifedependent recreation, interpretation and 

education opportunities which foster 

an understanding of the Refuge’s unique 

wildlife and plant communities in an urban 

setting. 

Objective 3.A: Within the next five years, 

recruit and maintain sufficient short and 

long term volunteers to accomplish three 

habitat restoration projects, eight wildlife 

surveys, six environmental education 

programs, and remain active in offering a 

variety of other volunteer opportunities. 

Rationale: Refuge volunteer programs are 

a vital instrument for providing educational 

and interpretive opportunities to the 

public and for assisting with biological 

monitoring and visitor use programs. The 

reauthorization of the National Wildlife 

Refuge Volunteer and Community 

Partnership Enhancement Act of 1998 

illustrates the importance of volunteer 

programs and community partnerships in 

helping to fulfill the mission of the National 

Wildlife Refuge System. 

Strategies:

1. Broaden the scope of volunteer tasks 

and define volunteer positions to 

better utilize the diverse interests, 

talents and abilities of residents in the 

surrounding communities. 

2. Develop a Refuge volunteer manual 

to aid the volunteer coordinator 

with planning and implementing the 

volunteer program.

3. Provide at least one comprehensive 

volunteer training opportunity per 

year with a revised and updated 

volunteer training manual and other 

educational opportunities.

4. Develop and maintain a volunteer 

database.

5. Pursue opportunities to collaborate 

on expanding volunteer activities with 

the Sacramento Regional County 

Sanitation District, Cosumnes River 

Preserve and Delta Meadows State 

Park.

6. Recruit Student Conservation 

Association, AmeriCorps, California 

Conservation Corps and other interns 

to work in a variety of programs.

7. Explore and continue ongoing outreach 

efforts to recruit quality volunteers.

8. Expand opportunities for specific 

one-time volunteer events, ongoing 

individual opportunities and ongoing 

group opportunities, including 

community service hour use 

opportunities.

9. Continue and expand volunteer 

participation in three habitat 

restoration projects on the 

Headquarters Unit, including 176 

acres of managed and passive seasonal 

and permanent wetlands, 82 acres 

of wet meadow and upland native 

grasslands and 83 acres of riparian 

habitats.

10. Maintain and expand volunteer 

participation in eight ongoing 

wildlife monitoring surveys including 

waterbird monitoring, nest box 

monitoring, rookery surveys, landbird 

mistnetting/disease monitoring, 

sandhill crane surveys, grasslands 

monitoring, frog malformation survey 

and Swainson’s hawk/burrowing 

survey.

11. Maintain and expand volunteer 

participation in six environmental 
Stone Lakes NWR Comprehensive Conservation Plan 87

education programs including school 

groups, special group tours, partnering 

with schools on curricula, special 

events, volunteer work and teacher 

workshops. 

Objective 3.B: Construct adequate 

facilities and develop programs for 

visitors to visit the Refuge seven days a 

week to observe, photograph and enjoy 

the Refuge’s unique natural habitats and 

wildlife during all seasons of the year 

with a target of 10,500 visit opportunities 

per year by 2009.

Rationale: Wildlife observation and 

photography are two of the six priority 

visitor uses identified in the National 

Wildlife Refuge System Improvement Act 

of 1997. These wildlife dependent activities 

were identified in the EIS (USFWS 1992) 

and should be offered on the Refuge. 

Currently, the Refuge has limited visitor 

access to two days per month and, as a 

result, the expectations of the visiting public 

are not being met A great potential also 

exists to provide visitors opportunities for 

wildlife observation and photography from 

boats. To prevent disturbance of wildlife, 

boats would be limited to using trolling 

motors. A no-wake zone on the entire 

Refuge would minimize conflicts with other 

users, water quality degradation, erosion to 

levees and disturbance to wildlife. Boating 

would be allowed from June to September 

to minimize impacts to heron rookeries and 

Swainson’s hawks nesting along riparian 

corridors.

Strategies:

1. Construct two photography blinds on 

the Headquarters and North Stone 

Lake units.

2. Construct restrooms on the Beach 

Lake, Headquarters and South Stone 

Lake units.

3. Construct two miles of universally 

accessible trails and 200 feet of 

boardwalk on the Headquarters Unit. 

4. Construct a safe entrance road and 

parking area for approximately 40 

vehicles on the Headquarters Unit 

5. Construct a viewing platform on the 

Headquarters Unit overlooking newly 

constructed wetlands.

6. Construct a safe vehicular access point, 

a parking area for 15 cars and a trail 

and a wildlife observation platform 

Wildlife observation 

and photography 

are two of the six 

priority public uses 

identified in the 

National Wildlife 

Refuge System 

Improvement Act of 

1997.

Photo by USFWS
88 Stone Lakes NWR Comprehensive Conservation Plan

on the southern portion of the North 

Stone Lake Unit, accessible from 

Hood-Franklin Road. Design and 

locate facilities to minimize impact on 

sandhill cranes, arctic nesting geese, 

giant garter snakes and burrowing 

owls. 

7. Provide parking for approximately 

20 cars at the boat launch on the 

South Stone Lake unit to provide 

wildlife viewing, photography, 

fishing and associated cartop boating 

opportunities. Only non-motorized 

or electric motor-only boats would be 

allowed on South Stone Lake from 

June through September. South Stone 

Lake would be an enforced no-wake 

zone.

8. Construct 1.5 miles of foot trails and 

200 feet of boardwalk on the South 

Stone Lake unit open to the public 

seven days a week with seasonal 

restrictions.

9. Develop a boat-accessible haul-out 

site, walking trail and viewing blind on 

the South Stone Lake Unit (i.e., Lodi 

Peninsula)..

10. Provide parking and boat launch 

capacity for approximately 10 cartop 

boats (including canoes and kayaks) 

on the Beach Lake unit at the end of 

Elliott Ranch Road to provide wildlife 

viewing, photography and fishing 

opportunities for pre-registered 

groups in SP Cut from June through 

September.

11. Once visitor use facilities are made 

available on the Headquarters unit, 

shift the focus of the Beach and North 

Stone Lake units within one year from 

open-touring days to pre-registered 

school and docent-guided tour groups. 

12. Develop guided tours for the Wetland 

Preserve Unit. 

13. Restrict land-based visitor use near 

habitat suitable for heron/egret 

rookeries, nesting Swainson’s hawks 

and other areas used by nesting 

migratory birds during sensitive laying 

and incubation periods (approximately 

February to June 15). 

14. Minimize disturbance to sandhill crane 

foraging and roosting habitats on the 

Refuge by restricting public access 

during October through March. 

15. Reduce potential spread of invasive 

species by visitors by restricting 

access to paved or graveled trails and 

maintaining trails in good condition 

through regular weed control.

Objective 3.C: Within five years, develop 

an environmental education program 

with a target of providing 80 opportunities 

per year for groups with an outdoor 

experience where visitors become aware 

of the Refuge’s role in the conservation 

of Central Valley and Sacramento San 

Joaquin Delta habitats and their fish and 

wildlife.

Rationale: Environmental education is 

one of the six priority visitor uses identified 

in the National Wildlife Refuge System 

Improvement Act of 1997. The Refuge 

provides a unique opportunity for the local 

community to experience Central Valley 

habitats and wildlife in proximity to an 

urban area. Refuge-based environmental 

educational activities can also be integrated 

into both indoor and outdoor classroom 

curriculums.

Strategies:

1. Offer up to four staff and/or docent 

lead environmental education tours on 

the Refuge per week.

2. Within five years, conduct 

teacher workshops to develop an 

environmental education program 

featuring teacher lead tours with a 

target of training six to 12 groups of 

teachers per year.

3. Develop a Junior Biologist Trail as 

part of the proposed Blue Heron Trail 

System on the Headquarters Unit to 

be used by schools and other groups 

and individuals.

4. Develop a Refuge elementary school 

curriculum manual for teachers to use 

while visiting the Refuge that includes 

pre- and post-visitation activities.

5. Explore feasibility of a Refuge fee area 

to support environmental education 

programs and general maintenance of 
Stone Lakes NWR Comprehensive Conservation Plan 89

visitor use areas.

Objective 3.D: Within five years, develop 

two interpretive programs where 

visitors could learn of the Refuge’s 

role in conserving the Central Valley 

and Sacramento-San Joaquin Delta 

habitats and their fish and wildlife, 

with an emphasis on outdoor hands-on 

experiences.

Rationale: Interpretation is one of the six 

priority visitor uses identified in the National 

Wildlife Refuge System Improvement 

Act of 1997. Interpretive activities can 

introduce the public to the Refuge’s habitat 

management activities and familiarize them 

with the conservation efforts that protect 

local natural resources.

Strategies:

1. Develop a self-guided trail as part 

of the proposed Blue Heron Trails 

System on the Headquarters Unit with 

hands-on learning stations within two 

years.

2. Develop a class/group staging area 

and 5 open air interpretive shelters 

with one kiosk and exhibits as part 

of the Blue Heron Trails system that 

would accommodate approximately 40 

children at a time.

3. Develop interpretive displays on the 

Headquarters Unit that illustrate 

traditional dwellings, various 

subsistence strategies and the overall 

lifestyle of local American Indian 

Tribes (see Objective 4.F).

4. Continue existing guided hikes and 

offer one additional interpretive docent 

guided hike per month.

5. Develop interpretive panels and 

exhibits on South Stone Lake Unit.

6. Develop self-guided trail and 

interpretive displays for the Wetland 

Preserve Unit.

7. Develop a variety of written 

interpretive materials such as 

brochures, flyers and handouts 

 

Objective 3.E: Within five years, the 

Refuge will provide safe, boat-only 

fishing with day use parking facilities 

to accommodate approximately 20 boats 

on South Stone Lake and approximately 

ten boats on SP Cut from June through 

September. 

Rationale: Fishing is one of the six priority 

visitor uses identified in the National 

Wildlife Refuge System Improvement Act 

of 1997. Fishing has traditionally occurred 

on South Stone Lake and surrounding Delta 

waterways since American Indians occupied 

the area. In this objective, “safe,” is defined 

as the absence of any fishing-related safety 

incidents.

Strategies: 

1. Develop and maintain a safe public 

parking lot and boat launch facilities 

to accommodate approximately 20 

cartop (not trailered) boats on the 

South Stone Lake unit, including an 

informational kiosk with maps and 

brochures on regulations, health 

warnings, species identification and 

Refuge boundaries. Boating will 

extend up the SP Cut to the culvert on 

the South Stone Lake unit.

2. Provide a launch for pre-registered 

canoe/kayak groups in SP Cut on the 

Beach Lake unit from June through 

September. Access would be from the 

end of Elliott Ranch Road and a no 

wake zone will be enforced.

3. Fishing will be in accordance with all 

State regulations. Fishing will not 

include take of frogs or crayfish and 

will only be done with rod and reel.

4. Restrict water-based visitor use 

near habitat suitable for heron/egret 

rookeries and Swainson’s hawks 

during sensitive laying and incubation 

periods (approximately February to 

June 15). 

5. Develop facilities for mobility impaired 

persons to enter and exit canoes and 

kayaks safely.

6. See objective 3.B for other strategies 

related to opportunities for boating 

programs.

Objective 3.F: Continue to expand the 

Refuge outreach program, targeting the 

local community and nontraditional 
90 Stone Lakes NWR Comprehensive Conservation Plan

users, by expanding partnerships for 

the annual Walk on the Wildside event 

and prepare for a minimum of four 

appropriate off-Refuge events, per year, to 

increase awareness of the Refuge’s role in 

conserving Central Valley and Sacramento 

San Joaquin Delta habitats and their 

associated fish and wildlife.

Rationale: Environmental education is 

one of the six priority visitor uses identified 

in the National Wildlife Refuge System 

Improvement Act of 1997. The urban 

location of the Refuge provides opportunities 

for the Service to educate broader audiences 

within the local community, including 

nontraditional users, about the Refuge’s role 

in conserving Central Valley habitats and 

wildlife and the benefits the Refuge provides 

to the surrounding communities and Central 

Valley. 

Strategies:

1. Maintain Refuge website for a one-stop 

source of information about Refuge 

history, events and biological resources 

with links to the Stone Lakes National 

Wildlife Refuge Association and other 

partners.

2. Continue and expand partnerships 

for the annual Walk on the Wildside 

festival to celebrate the National 

Wildlife Refuge System and other 

events, such as International 

Migratory Bird Day.

3. Participate in at least four appropriate 

local off-refuge events each year, such 

as the Lodi Crane Festival and Salmon 

Festival. 

4. Support the Stone Lakes National 

Wildlife Refuge Association by 

actively participating in their events, 

activities and meetings and making 

monthly contributions to Association 

outreach related materials, including 

newsletters, the website and 

brochures.

5. Collaborate with and assist local 

resource-oriented agencies and 

city departments, such as the Elk 

Grove Community Service District, 

on outreach programs involving the 

Refuge. 

6. Develop new portable refuge displays 

for use at fairs, shows and festivals.

7. Expand the number of presentations 

given to schools, conservation groups 

and public service organizations.

Goal 4. In cooperation with tribal 

representatives, identify and protect 

cultural resources on the Refuge and 

educate the public regarding American 

Indians and the history of the region. 

Objective 4.A: Prepare a cultural 

resources overview of the Refuge, within 

15 years of CCP approval.

Rationale: Although record searches have 

been conducted for all Service-managed 

properties, a complete compilation of site 

records and relevant reports summarizing 

the number and locations of all recorded 

sites within the approved Refuge boundary 

would aid in planning land conservation, 

management and landowner outreach. 

Refuge planning efforts would be enhanced 

by identifying the location and composition 

of collections of human remains, funerary 

objects, sacred objects, or objects of cultural 

patrimony that were discovered and 

removed from within the approved Refuge 

boundary prior to the Service assuming 

land management authority. However, this 

overview would be for the sole purpose of 

identifying cultural resources and these 

collections would not fall under Service 

jurisdiction. 

Strategies:

1. Compile and maintain all existing 

baseline data on cultural resources 

sites, surveys and reports within one 

mile of the approved Refuge boundary.

2. In consultation with archaeologists and 

tribal representatives, approximate 

the location of unrecorded sites and 

culturally sensitive areas within the 

approved Refuge boundary by using 

site records, maps and other data. 

Identify cultural resources issues and 

needs and draft potential solutions. 
Stone Lakes NWR Comprehensive Conservation Plan 91

3. To aid with Refuge planning, identify 

the location and composition of any 

collections of human remains and 

Native American Grave Protection 

and Repatriation Act (NAGPRA) 

covered items removed from within 

the approved Refuge boundary prior 

to the Service’s assumption of land 

management.

Objective 4.B: Within 15 years of CCP 

approval, evaluate conditions of known 

cultural resource sites on Refuge managed 

lands and conduct seasonal monitoring of 

known sites.

Rationale: The Service is required to 

ensure that the integrity of any cultural sites 

on Refuge lands are protected. As a result 

of the activities of previous landowners, 

sites may have been impacted or may still 

be vulnerable to continued degradation 

(e.g.,erosion, traffic, theft). Therefore, 

sites should be evaluated by qualified 

professionals and measures to stop and/or 

reverse deterioration of the sites should be 

developed and implemented. 

Strategies:

1. Conduct monthly monitoring visits of 

known cultural resource sites on the 

North Stone Lake Unit to ensure that 

existing grazing protection measures 

are intact. 

2. As needed, consult with professional 

archaeologists, local tribal 

representatives and the Regional 

Office Archaeologist regarding any 

necessary protection or remediation 

measures for cultural resource sites. 

3. Develop additional measures to protect 

sites and/or remediate past damages, if 

necessary.

Objective 4.C: Identify and delineate any 

cultural resources on new lands coming 

under Refuge management. 

Rationale: Identifying historic properties 

on lands as they come under Refuge 

management will enable staff to ensure that 

any restoration and management programs 

for fish and wildlife will also protect the 

integrity of sensitive cultural resources. 

Strategies:

1. As funding is available, a qualified 

archeologist will survey new properties 

coming under Refuge management 

to locate and delineate, as needed, 

any known or previously unrecorded 

cultural resource sites.

2. In consultation with the appropriate 

Service or other professional cultural 

resource experts, evaluate sites on 

newly-managed properties to identify 

any protection, restoration, and/or 

management measures that may be 

necessary. 

Objective 4.D: Meet annually with the 

Ione Band of Miwok Indians and other 

concerned tribal groups to discuss land 

management and restoration activities 

planned for the upcoming field season. 

Rationale: The Service has agreed to 

meet annually with the Ione Band of Miwok 

Indians to keep them informed regarding 

planned Refuge activities. Meetings will also 

provide a forum for tribal representatives 

to present any of their proposals or discuss 

other concerns that relate to management of 

Refuge lands. 

Strategies:

1. As the Service has previously agreed, 

hold an annual meeting to review 

previous projects or summarize 

management or restoration projects 

and public events that are planned 

by the Refuge for the upcoming 

year, whether or not these activities 

will require formal State Historic 

Preservation Office consultation. 

2. Review and reissue, if appropriate, 

any special use permits for traditional 

activities such as plant collecting for 

basket weaving.

Objective 4.E: Within five years, 

begin developing a memorandum of 

understanding or agreement with the 

Ione Band of Miwok Indians or with other 

involved tribal organizations to facilitate 

compliance with the Native American 
92 Stone Lakes NWR Comprehensive Conservation Plan

Grave Protection and Repatriation Act 

(NAGPRA) and to establish protocols for 

treating human remains and associated 

funerary objects, sacred objects or objects 

of cultural patrimony. 

Rationale: Due to previous land uses, 

some Refuge lands and other properties 

within the approved Refuge boundary 

have human remains or NAGPRA covered 

items exposed on the surface of the ground. 

Currently, the Refuge consults with the 

Ione Band of Miwok Indians regarding 

land management programs and the status 

of burial sites. In addition to the Ione 

Band, other organizations may need to be 

consulted. In consultation with the Ione 

Band and other relevant authorities and 

experts, the Refuge has implemented some 

protection measures and assisted with some 

repatriation of human remains and funerary 

items. Since more sites are expected to 

come under Refuge management and to 

facilitate compliance with NAGPRA, a 

formal agreement with tribal groups should 

be developed to define the protocol to be 

followed when protection, repatriation and 

re-interment measures are appropriate. 

Strategies:

1. Develop an agreement that includes 

the following elements: notification 

procedures; when appropriate, 

procedures for collection of human 

remains and associated funerary 

objects, sacred objects, or objects 

of cultural patrimony; criteria for 

defining NAGPRA covered items; any 

data collection or study of materials 

that may be warranted; guidelines for 

any temporary or permanent curation 

of non-repatriated materials; and a reinterment protocol. 

Objective 4.F: Develop a minimum of two 

interpretive panels and exhibits, located 

various on units, to educate the public 

regarding the cultural resources of the 

Refuge and past and present American 

Indian cultural practices, within 15 years 

of CCP approval.

Rationale: Developing interpretive and 

educational materials to increase public 

understanding about local American Indian 

peoples is necessary, given the abundance 

of cultural resources within the approved 

Refuge boundary and the historic role of 

Indians in the Sacramento-San Joaquin 

Delta. These materials will aid Refuge staff 

in explaining historical ecological conditions, 

the importance of restoring and/or 

maintaining the integrity of those conditions 

and the role fish and wildlife played in 

American Indian culture and history. 

Strategies: 

1. Develop exhibits for the Headquarters 

and Beach Lake units to illustrate 

traditional dwellings, various 

subsistence strategies and the overall 

lifestyle of local American Indian 

peoples. 

2. Solicit input and advice from 

concerned tribal representatives in 

planning, information gathering and 

review of educational, interpretive and 

outreach programs and publications. 

Work with Tribes and universities to 

identify the messages and resources 

that would be most appropriate to 

share with the public.

3. In publications or exhibits, provide a 

brief history of the indigenous peoples 

of greater California, scaling down to 

the Sacramento Valley and then to the 

Sacramento-San Joaquin Delta region 

to educate the public. 

4. Include a cultural resource element in 

special events held on the Refuge.
Stone Lakes NWR Comprehensive Conservation Plan 93

6 Implementation and Monitoring

Once the preferred management alternative 

and CCP are finalized and approved and 

the Service has notified the public of its 

decision, the implementation phase of the 

CCP process begins. Implementation 

occurs over a period of 15 years, during 

which the CCP will serve as the primary 

reference document for all Refuge 

planning, operations and management until 

it is formally revised. The Service will 

implement the final CCP with assistance 

from existing and new partner agencies and 

organizations and from the public.

The activities required to realize the 

management goals discussed in this CCP are 

referred to as “projects” below. Every effort 

will be made to implement the projects by 

the established deadlines. However, the 

implementation timing of the management 

activities proposed in this document is 

contingent upon a variety of factors, 

including:

Completion of detailed step-down 

management plans 

Funding

Staffing

Compliance with other Federal laws and 

regulations

Partnerships

The results of monitoring and evaluation

Each of these factors is described briefly 

below as they apply to the Service’s 

proposed action.

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 

planning details necessary to implement 

•

•

•

•

•

•

management strategies identified in a 

CCP. Refuge staff members have already 

completed a number of step-down plans. 

These include fire management, grazing, 

land protection and mosquito integrated 

pest management plans. This CCP proposes 

several new step-down plans that are 

identified in Table 2, along with target dates 

for completion.

Funding and Staffing 

Resources are required to adequately 

operate any national wildlife refuge 

including initial capital outlay for equipment, 

facilities, labor and other expenses as 

well as recurring, annual costs for staff, 

contracts, supplies, maintenance and other 

recurring expenses (See Table 3, Estimated 

Initial Capital Outlay to Implement CCP). 

The estimated initial capital outlay for 

the Refuge, described in this CCP would 

cost approximately $10 million. Not all of 

these capital expenditures would occur in 

the same year as many of these expenses 

would be most likely implemented over 

the course of several years. The detailed 

descriptions of objectives and their 

associated implementation strategies serve 

as a guide to the ideal time frame in which 

to implement capital expenditures. The 

largest costs for initial outlays are for visitor 

Table 2. Step-down Management Plans 

Step Down Plan Target for Completion

Fisheries Management Plan 2008

Invasive Weed - Integrated Pest 

Management Plan

2008

Volunteer Plan 2009

Comprehensive Inventory and 

Monitoring Plan

2009

Habitat Management Plan 2009
94 Stone Lakes NWR Comprehensive Conservation Plan

services and habitat restoration as should be 

expected for an urban refuge. 

To fully implement this CCP, personnel 

dedicated to the Refuge would include: 

• 1 Project Leader

• 1 Deputy Project Leader

• 1 Wildlife Biologist

• 1 Administrative Support Assistant

• 1 Outdoor Recreation Specialist

• 1 Park Ranger

• 1 Motor Vehicle Operator

• 1 Engineering Equipment Operator

Annual contracts or cooperative agreements 

will also be needed to provide specialized 

services beyond the core Refuge functions, 

for which staff are required. The recurring 

staffing and other costs associated with 

CCP implementation total approximately 

six hundred and seventy thousand dollars 

(See Table 4, Estimated Annual Cost to 

Implement the CCP). This is approximately 

a 65 percent increase over the Fiscal Year 

2006 operations budget of 435,000. 

Compliance Requirements

This CCP was developed to comply with 

all Federal laws, executive orders and 

legislative acts to the extent possible. Some 

activities , particularly those that involve 

revising an existing step-down management 

plan or preparing a new one, would need to 

comply with other laws or regulations. In 

addition to NEPA and the Improvement Act, 

full implementation of all components of this 

CCP would require compliance with:

• Executive Order 11988 (Floodplain 

Management)

• Executive Order 12372 

(Intergovernmental Review of Federal 

Programs)

• Executive Order 11593 (Protection of 

Historical, Archaeological, and Scientific 

Properties)

• Executive Order 11990 (Protection of 

Wetlands)

• Executive Order 12996 (Management 

and General Public Use of the National 

Wildlife Refuge System)

• Executive Order 12898 (Environmental 

Justice in Minority Populations and LowIncome Populations)

• Secretarial Order 3127 (Hazardous 

Substances Determinations)

• Endangered Species Act of 1973, as 

amended

• Refuge Recreation Act of 1962, as 

amended

• National Historic Preservation Act of 

1966, as amended

Partnership Opportunities 

As described in Chapter 1, a wide array 

of private and public partners play an 

important role in helping the Service 

achieve its goals and objectives for the 

Refuge. The Service will continue to rely 

on these and other partners in the future 

to help implement the final CCP and to 

provide input for future CCP updates. This 

draft CCP identifies many projects that 

provide new opportunities for existing or 

new partners. There is great potential for 

more public participation and assistance 

in the management and interpretation of 

the Refuges. The Service welcomes and 

encourages more public participation in the 

Refuges.

Adaptive Management 

This draft CCP provides for adaptive 

management of the Refuge. Adaptive 

management is a flexible approach to 

long-term management of biotic resources 

that is directed by the results of ongoing 

monitoring activities and new data. 

Management techniques, objectives and 

strategies are regularly evaluated in 

light of monitoring results, new scientific 

understanding and other new information. 

These periodic evaluations are used to adapt 

management objectives and techniques 

to better achieve the Refuge’s goals. 

Monitoring is an essential component of 

adaptive management in general and of this 

draft CCP. Specific monitoring strategies 

have been integrated into the goals and 

objectives whenever possible.

Plan Amendment and Revision 

Refuge CCPs are meant to evolve with each 

individual Refuge unit. The Improvement 

Act specifically requires that CCPs be 

formally revised and updated at least every 

15 years. The formal revision process will 
Stone Lakes NWR Comprehensive Conservation Plan 95

follow the same steps as the CCP process 

(see Chapter 2: The Planning Process). In 

the meantime, the Service will annually 

review a checklist of the goals, objectives 

and management strategies of this CCP to 

assist in tracking and evaluating progress. 

The final CCP would also be informally 

reviewed by Refuge staff while preparing 

annual work plans and updating the Refuge 

database. 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 the final CCP 

would not change until they are re-evaluated 

as part of the formal CCP revision process. 

The objectives and strategies, however, 

may be revised to address changing 

circumstances or to take advantage of 

increased knowledge of the resources on the 

Refuge. If changes are required, the level 

of public involvement and associated NEPA 

documentation would be determined by the 

Refuge Manager, in accordance with Service 

policy.
Table 3. Estimated Initial Capital Outlay to Implement the CCP

Expenditure (Related Strategy) Unit Cost Unit Quantity Total Cost

Plant trees with beaver exclusion fences (1.A.1) $15,000 mile 1.3 $19,500

Expand riparian zone at S. Stone Lakes and HQ (1.A.2) $6,000 acre 5 $30,000

Restore 20 acres by HQ to native plants (1.A.3) $8,000 acres 20 $160,000

Enhance sub-canopy in BL, NSL units (1.A.4) $3,000 acre 115 $345,000

Establish native plant nursery by HQ (1.A.5) $65,399 ea 1 $65,399

Plant early/mid-seccessional vegetation on west portion of the SSL 

Unit (1.A.6)

$6,000 acre 126 $756,000

Maintain/expand fencing along SP cut (1.B.3) $10,000 mile 1.3 $13,000

Modify existing water delivery system on SSL Unit (1.C.1) $25,000 mod. 1 $25,000

Map elodea at SSL and initiate control (1.G.3) $10,000 $10,000

Enhance burrowing owl habitat at NSL unit (1.H.4) $15,000 exp. unit 1 $15,000

Establish experimental native grass plots (1.J.1) $8,000 acre 0.25 $2,000

Restore Beach Lake Unit grasslands (1.J.5) $8,000 acre 108 $864,000

Develop a levee and flood control channel maintenance MOU (1.M.4) $20,000 program 

dev.

1 $20,000

Develop a Refuge volunteer manual (3.A.2) $19,505 ea 1 $19,505

Develop a Refuge volunteer database (3.A.4) $19,505 ea 1 $19,505

Construct photography blinds (3.B.1) $15,000 ea 2 $30,000

Construct restrooms at BL, SSL and HQ (3.B.2) $50,000 ea 3 $150,000

Construct 2 miles of universally accessible trails at HQ Unit (3.B.3) $100,000 mile 2 $200,000

Construct 200 ft. boardwalk at HQ (3.B.3) $1,060 feet 200 $212,000

Construct entrance road and parking area (3.B.4) $1,500,000 ea 1 $1,500,000

Construct viewing platform and associated boardwalk on HQ site 

(3.B.5)

$500,000 ea 1 $500,000

Construct parking lot, trail and observation platform at NSL site 

(3.B.6)

$620,000 ea 1 $620,000

Improve entrance road and parking area at SSL boat launch site 

(3.B.7)

$1,000,000 ea 1 $1,000,000

Construct foot trails at SSL (3.B.8) $100,000 mile 1.5 $150,000

Construct 200 ft. boardwalk at SSL (3.B.8) $1,060 feet 200 $212,000

Develop boat haul out and assoc. trail at Lodi Gun Club (3.B.9) $30,000 ea 1 $30,000

Improve parking at BLU Lewis tract at end of Elliott Ranch Road 

(3.B.10)

$163,000 ea 1 $163,000

Develop a Junior Biologist Trail at HQ complete with entrance 

signs, universally accessible trails, entrance kiosk, interpretive 

panels (3.C.3, 3.D.1)

$1,630,000 ea 1 $1,630,000

Develop a an EE elementary school curriculum (3.C.4) $19,505 ea 1 $19,505

Develop open air shelters (5) and main shelter (3.D.2) $50,000 ea 6 $300,000

Develop local Indian displays at HQ (3.D.3, 4.F.) $50,000 ea 1 $50,000

Develop interpretative panels at SSL (3.D.5) $50,000 ea 1 $50,000

Develop self-guided trail and interpretative displays for the 

Wetlands Preserve Unit (3.D.6)

$300,000 ea 1 $300,000

Develop written interpretative materials (3.D.7) $19,505 ea 1 $19,505
Expenditure (Related Strategy) Unit Cost Unit Quantity Total Cost

Develop parking lot and boat launch at SSL (3.E.1) $55,000 ea 1 $55,000

Develop disabled accessible boating facilities (3.E.5) $50,000 ea 1 $50,000

Compile baseline cultural resources data (4.A.1) $5,000 ea 1 $5,000

Locate unrecorded cultural sites and sensitive areas (4.A.2) $5,000 ea 1 $5,000

Identify location of human remains and NAGPRA items located in 

collections and museums (4.A.3)

$5,000 ea 1 $5,000

Develop exhibits for the HQ and BL units to illustrate traditional 

dwellings, subsistence strategies and lifestyle (4.F.1)

$25,000 ea 2 $50,000

Total $9,669,919

Table 4. Estimated Annual Cost to Implement the CCP

Expenditure (Related Objective) Unit Cost Unit Quantity Total Cost

Staff Salaries and Benefits (# indicates position filled)

 # Refuge Refuge Manager/PL - GS-13 $102,450 ea 1 $102,450

 # Refuge Assistant Refuge Manager - GS -12 $84,032 ea 1 $84,032

 Wildlife Biologist GS-9 $65,680 ea 1 $65,680

 # Administrative Support Assistant - GS-7 $54,268 ea 1 $54,268

 # Outdoor Recreation Planner GS-11 $70,122 ea 1 $70,122

 Park Ranger GS-7 $47,372 ea 1 $47,372

 Engineering Equipment Operator - WG - 8 $53,560 ea 1 $53,560

 # Motor Vehicle Operator WG - 6 $46,540 ea 1 $46,540

Maintenance supplies (1.D., 1.H., 1.F.) $50,000 1 1 $50,000

Invasive weed management program (1.A., 1.B., 1.D., 1.E., 1.F., 1.H.) $60,000 ea 1 $60,000

Water/pumping cost (1.I., 2.A.) $20,000 ea 1 $20,000

Maintain 40-60 acres or agricultural fields (2.A.5) $5,000 ea 1 $5,000

Levee and flood control channel maintenance MOU coordination 

(1.M.4)

$10,000 ea 1 $10,000

Water quality monitoring (1.N.) $60,000 ea 1 $60,000

Travel/training $6,000 ea 1 $6,000

Supplies $25,000 ea 1 $25,000

Printing $5,000 ea 1 $5,000

Pump-out for restroom $5,000 ea 1 $5,000

Total $667,574

Table 3. (continued)
98 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 99

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of California and Southern Oregon. Sacramento, CA.

http://www.fws.gov/sacramento/es/recovery_plans/vp_recovery_plan_links.htm 

Viewed on June 26, 2006.

Vanicek, C. David. 1992. Memorandum, Dec 2, 1999 to Tom Harvey.

Wylie 1997. Biological Resources Division (BRD) survey for the giant garter snake.
Stone Lakes NWR Comprehensive Conservation Plan 105

Personal Communications

Geupel, Geoff. Point Reyes Bird Observatory (PRBO). 2003.

Ivey, Gary. Private Consultant. 2003. 

Marty, J. 2004. Biological Resources Division (BRD). Science Talk, September 2004.

Treiterer, Beatrix. U.S. Fish and Wildlife Service (USFWS). September 2004, July 2006.
106 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 107

Appendices
108 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 109

Appendix A. Compatibility Determinations

Compatibility Determination for Recreational Fishing on the Stone Lakes National 

Wildlife Refuge

Use: Fishing

Refuge Name:

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s):

Stone Lakes NWR purposes include:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. § 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. § 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. § 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. § 715d (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. § 1534 (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: The mission of the National Wildlife Refuge 

System (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” (National Wildlife Refuge System Administration Act of 1966, as 

amended [16 U.S.C. 668dd-668ee]).
110 Stone Lakes NWR Comprehensive Conservation Plan

Description of Use: 

Fishing is one of six priority public uses (i.e., hunting, fishing, wildlife observation, 

photography, environmental education and interpretation) identified in the National Wildlife 

Refuge System Improvement Act of 1997. Fishing has occurred within the Stone Lakes 

Basin and surrounding Delta waterways since prior to European settlement of the region. 

The visitor use program in the CCP proposes to open portions of the Refuge to fishing 

from boats from June through September and to expand visitor opportunities for wildlifedependent recreation (USFWS 2006a). Due to limitations in parking space, launching 

sites, and the navigability of Refuge waterways, only cartop, hand-launched boats, such 

as canoes and kayaks will be permitted. Gas-powered outboard motors will not be allowed 

and a no wake zone will be enforced but use of electric motors will be possible in the South 

Stone Lake unit. Fishing will not include take of frogs or crayfish and will only be with 

rod and reel. The Service does not intend to allow bank fishing on the Refuge, due to a 

number of concerns, including: erosion of banks and other habitat impacts from trampling of 

vegetation, lack of staff to monitor use, and lack of infrastructure such as piers or platforms. 

Game fish species to be allowed for legal take will include all native and introduced species 

listed in the California Freshwater Sport Fishing Regulations (e.g., bass, catfish, crappie, 

bluegill, sunfish, shad, carp). Fishing will be permitted in accordance with State and Federal 

regulations to ensure it will not interfere with conservation of fish and wildlife and their 

habitats. An informational kiosk with maps and brochures on regulations, health warnings, 

species identification, and Refuge boundaries will be available near the boat launch area. 

Chapter 5 of the Comprehensive Conservation Plan, Refuge Vision, Goals and Objectives, is 

herein incorporated by reference. 

Availability of Resources: 

Staff necessary to oversee the Refuge fishing program will be shared with other programs 

as described in the Draft Stone Lakes NWR CCP (USFWS 2006a). Shared staff member(s) 

would be sufficient to operate the modest program described in this plan. Facilities to 

support the program will require capital outlays and recurring costs however, some of the 

costs will be available through other visitor use programs, such as wildlife observation and 

photography. If unexpected costs arise, such as the need for more enforcement or higher 

than expected maintenance needs, we will reevaluate the program and make necessary 

adjustments, such as seeking volunteers or other partnerships to maintain facilities and 

administer the program. 

Item One Time Cost Recurring Costs

Boat Ramp $30,000 $5,000

Parking Area $20,000 $5,000 

Maintenance of Parking Lots 

 and Boat Launches N/A $5,000

Maintenance (0.50 FTE) $26,000 $26,000

Restroom $50,000 $2,000

Law Enforcement (0.50 FTE) $25,000 $25,000

Administration $2,000 $2,000

TOTAL $153,000 $70,000

Anticipated Impacts of the Use(s): 

Impacts are discussed in detail in the environmental assessment for the Draft 

Comprehensive Conservation Plan (USFWS 2006). Fishing and other human activities may 

cause disturbance to wildlife (Burger 1981) and the cumulative effects of this expanded use 

will likely have effects on habitat and the fisheries resource (Buckley and Buckley 1976, 

Glinski 1976, Miller et al. 1998, Reijnen and Foppen 1994, Smith and Hunt 1995). Fishing 
Stone Lakes NWR Comprehensive Conservation Plan 111

may result in increased problems with vandalism and litter such as discarded monofilament 

line and tackle. Because few native fish species are found at Stone Lakes, and non-native 

game species are plentiful, the impact on the native fishery is not expected to be significant.

Federally-listed species that may occur on the Refuge include the giant garter snake, 

valley elderberry longhorn beetle, and the vernal pool tadpole and fairy shrimp (USFWS 

2006b). No impacts to vernal pool species are anticipated from fishing because fishing will 

be permitted only on waterways of the Beach Lake, North Stone Lake and South Stone 

Lake units where there are no vernal pools. State-listed species that may inhabit the 

Refuge include greater sandhill crane and Swainson’s hawk. The most sensitive period for 

Swainson’s hawk is during the nesting season, typically mid-February through July. Likely 

nesting areas would be closed to visitors during the nesting season. Impacts to greater 

sandhill cranes are not anticipated since the fishing season does not coincide with wintering 

crane use at the Refuge. 

The following measure will be taken to avoid impacts to fish and wildlife:

• Provide printed materials to inform anglers about fishing regulations and boundaries of 

fishing areas; 

• Maintain parking areas, roads, and boat launches to prevent erosion or habitat damage;

• Monitor fishing to ensure that facilities are adequate and wildlife disturbance is minimal;

• Prohibit gas-powered watercraft to protect water quality and submerged vegetation;

• Implement a seasonal closure from October through May to reduce disturbance to 

wintering, nesting, resting, and foraging birds and other wildlife, their habitats, and public 

engaged in other wildlife-dependent uses;

• Prohibit watercraft within 0.25 miles of occupied Swainson’s hawks nests until the young 

have fledged (i.e., 2nd half of July);

• Refuge law enforcement staff will randomly check anglers for compliance with state 

fishing laws and refuge-specific fishing regulations; and

• Comply with all measures identified in the CCP Section 7 Consultation to minimize or 

eliminate conflicts with federally-listed or non-target species.

Public Review and Comment: One person commented that bank fishing requires no 

additional staff and should be allowed.

Response: Allowing bank fishing would require additional staff effort based largely on the 

need for regular trash removal and public safety associated with bank fishing on the Refuge. 

A step-down fisheries management plan is proposed for completion in 2008 (page 95 of the 

CCP), which will address management of fishing on the Refuge possibly including bank 

fishing.

Determination (check one below): 

_____ Use is Not Compatible

 X Use is Compatible with the Following Stipulations

Stipulations Necessary to Ensure Compatibility: 

Fishing will be permitted at Stone Lakes NWR with the following stipulations:

• Fishing will be conducted exclusively from boats

• No trailered boats will be permitted. Cartop, hand-launched boats with or without electric 

motors will be permitted; gas motor boats will not allowed;

• No vehicles will be allowed in boat launch areas;

• All closed areas will be identified in printed materials provided to anglers and posted and 
112 Stone Lakes NWR Comprehensive Conservation Plan

patrolled to prevent trespass through adjacent properties; 

• Littering regulations will be strictly enforced; 

• Use or possession of alcohol while sport fishing will be prohibited;

• No building or maintaining of fires will be permitted on the Refuge;

• The western portion of the South Stone Lake Unit will be closed to fishing during the 

waterfowl hunting season; and 

• Fishing will be allowed during daytime hours only.

The Refuge Manager will have authority to close certain areas during critical wildlife use 

periods and cancel any activities deemed necessary to fulfill Refuge purposes or ensure 

visitor safety. Sensitive nesting areas will be protected from disturbance by visitors 

with signs and barriers. Visitors will be directed away from areas where major habitat 

restoration or management projects are under way. 

Justification: 

Fishing is an appropriate wildlife-dependent recreational activity. Based upon biological 

impacts described in the Refuge Draft Comprehensive Conservation Plan and 

environmental assessment, it is determined that fishing within the Refuge will not materially 

interfere with or detract from the purposes for which the Refuge was established.

Fishing is a priority wildlife-dependent visitor use provided for in the National Wildlife 

Refuge System Improvement Act of 1997. By facilitating this use on the Refuge, we hope 

to increase the visitors’ knowledge and appreciation of fish and wildlife, which may lead 

to increased public stewardship of wildlife and their habitats on the Refuge. Increased 

public stewardship will support and complement the Service’s actions in achieving the 

Refuge’s purposes and the mission of the National Wildlife Refuge System. This program 

as described is determined to be compatible and will not conflict with the national policy to 

maintain the biological diversity, integrity, and environmental health of the refuge.

Mandatory Reevaluation Date (provide month and year):

 February, 2022 Mandatory 15-year Reevaluation Date (for priority public uses)

_________ Mandatory 10-Year Reevaluation Date (for all uses other than priority 

 public uses)

 

NEPA Compliance for Refuge Use Decision (check one below):

Conducted with Comprehensive Conservation Plan

______ Categorical Exclusion without Environmental Action Statement

______ Categorical Exclusion and Environmental Action Statement

 X CCP Environmental Assessment and Finding of No Significant Impact

______ Environmental Impact Statement and Record of Decision

References Cited:

Buckley, P. A. and F. G. Buckley. 1976. Guidelines for protection and management of 

colonially nesting waterbirds. North Atlantic Regional Office, National Park Service, 

Boston, MA. 52pp.
Stone Lakes NWR Comprehensive Conservation Plan 113

Burger, J. 1981. The effect of human activity on birds at a coastal bay. Biol. Cons. 21:231-

241.

Glinski, R. L. 1976. Bird watching etiquette: the need for a developing philosophy. Am. 

Bird 30(3):655-657.

Miller, S. G., R. L. Knight, and C. K. Miller. 1998. Influence of recreational trails on 

breeding bird communities. Ecol. Appl. 8:162-169.

Reijnen, R. and R. Foppen. 1994. The effects of car traffic on breeding bird populations 

in woodland. I. Evidence of reduced habitat quality for willow warbler (Pylloscopus 

trochilus) breeding close to a highway. J. Appl. Ecol 31: 85-94.

Smith, L. and J. D. Hunt. 1995. Nature tourism: impacts and management. Pp. 203-219 

in Knight, R. L.; Gutzwiller, K. J. (Wildlife and recreationists: coexistence through 

management and research, eds.). Island Press, Washington, D. C. 

U.S. Fish and Wildlife Service (USFWS). 2006a. Stone Lakes National Wildlife Refuge 

Draft Comprehensive Conservation Plan and Environmental Assessment, 2006. U. S. 

Fish and Wildlife Service, Sacramento, California.

U.S. Fish and Wildlife Service (USFWS). 2002b. Biological Opinion for the Stone Lakes 

National Wildlife Refuge Comprehensive Conservation Plan. U.S. Fish and Wildlife 

Service, Sacramento, California.
114 Stone Lakes NWR Comprehensive Conservation Plan

Compatibility Determination for Wildlife Observation and Photography on the 

Stone Lakes National Wildlife Refuge

Use: Wildlife Observation and Photography

Refuge Name: 

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s):

Stone Lakes NWR purposes include:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. § 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. § 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. § 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. § 715d (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. § 1534 (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).

Description of Use(s): 

Wildlife observation and photography are two of the six priority visitor uses (e.g., hunting, 

fishing, wildlife observation and photography, environmental educations and interpretation) 
Stone Lakes NWR Comprehensive Conservation Plan 115

identified in the National Wildlife Refuge System Improvement Act of 1997. Currently, 

visitor access to Stone Lakes National Wildlife Refuge (Refuge) is limited to two days per 

month and as a result the expectations of the visiting public are not being met. The Refuge 

proposes to provide adequate facilities to observe, photograph and enjoy wildlife and natural 

habitats during daylight hours in all seasons of the year

The Refuge would provide opportunities for wildlife observation and photography by 

constructing approximately 4.6 miles of universally accessible trails on the Headquarters, 

North Stone Lake and South Stone Lake Units, two photography blinds and two viewing 

platforms, expanding entrance roads and parking areas, and by offering boat access and 

guided tours to areas of interest, including vernal pools and wetlands. For additional 

details about this proposed use, please see the Stone Lakes National Wildlife Refuge 

Final Comprehensive Conservation Plan (USFWS, 2006) which is herein incorporated by 

reference.

Availability of Resources: 

Staff necessary to oversee the wildlife observation and photography programs will be 

shared with other programs described in the 2006 Draft CCP for Stone Lakes NWR. To 

fully implement this program as described in the CCP, significant increases in staff and, 

capital outlays, and recurring costs will be necessary. Facilities and materials to support 

the program will require capital outlays and recurring costs, however, some of the costs will 

be shared with other visitor used programs. If unanticipated costs arise, the program will 

be reevaluated and necessary adjustments made such as seeking volunteer or cooperator 

assistance to maintain facilities or applying for educational grants. 

Item One Time Cost Annual Costs

Photo Blinds (HQ, North Stone Lake) $ 30,000 $ 2,500

Viewing Platforms (HQ, North Stone Lake) $620,000 $ 5,000

Parking Areas (HQ, North Stone Lake) $520,000 $ 5,000

Trails

2.6 miles at South Stone Lake Unit $150,000 $15,000

2 miles at Headquarters Unit $400,000 $10,000

Boardwalks

1500 feet at Sun River $1,590,000 $ 7,000

200 feet at HQ $200,000 $ 2,500

Entrance Road Sun River Property (BLU) $400,000 $ 5,000 

Restrooms (HQ, BLU) $150,000 $ 6,000

Park Ranger (0.5 FTE) $ 25,000 $ 5,000

Maintenance Staff (0.5 FTE) $ 26,000 $26,000

Administration $2,000 

TOTAL $4,113,000 $89,000

Anticipated Impacts of the Use(s): 

Human activity may disturb migratory birds utilizing the Refuge’s habitats for feeding or 

nesting. Off-trail human activity in habitat restoration areas can slow restoration efforts 

through soil compaction, vegetation trampling and the introduction of invasive plants. Litter 

discarded by visitors can entangle wildlife or be ingested, resulting in injury or death. The 

construction and maintenance of trails and boardwalks may impact soils, vegetation, and in 

some instances hydrology around the trails. This could include an increased potential for 

erosion, soil compaction (Liddle 1975), reduced seed emergence (Cole and Landres 1995), 

alteration of vegetative structure and composition and sediment loading (Cole and Marion 

1988).
116 Stone Lakes NWR Comprehensive Conservation Plan

Federally-listed species that may occur on the Refuge include the giant garter snake, valley 

elderberry longhorn beetle, vernal pool tadpole and fairy shrimp. No impacts to vernal pool 

species are anticipated from wildlife observation and photography. California state-listed 

species that inhabit the Refuge include greater sandhill crane and Swainson’s hawk. The 

primary disturbance season for Swainson’s hawk is during their nesting season, typically 

mid-February through July. Prime nesting habitat would be closed to visitors during the 

nesting season.

Of the wildlife observation techniques, wildlife photographers tend to have the largest 

disturbance impacts (Klein 1993, Morton 1995, Dobb 1998). While wildlife observers 

frequently stop to view species, wildlife photographers are more likely to approach wildlife 

(Klein 1993). Even slow approach by wildlife photographers tends to have behavioral 

consequences to wildlife species (Klein 1993). Other impacts include the potential for 

photographers to remain close to wildlife for extended periods of time, in an attempt to 

habituate the wildlife subject to their presence (Dobb 1998) and the tendency of casual 

photographers, with low-power lenses, to get much closer to their subjects than other 

activities would require (Morton 1995), including wandering off trails. This usually results 

in increased disturbance to wildlife and habitat, including trampling of plants. Impacts of 

wildlife observation and photography are also discussed in the Compatibility Determination 

for environmental education and interpretation.

Public Review and Comment: Many written and oral comments recommended that highspeed boating should not be allowed to continue on the refuge in part because it is disruptive 

of visitors participating in wildlife observation and photography on the refuge.

Response: High-speed boating was found to be not compatible through a Compatibility 

Determination. According to the compatibility policy (part 603 FW 2, 2.14) “Existing 

uses determined to be not compatible will be expeditiously terminated...this process of 

termination...will not exceed 6 months (without written authorization from the Director)..." 

The Refuge will follow the Service compatibility policy and eliminate high speed boating as 

expeditiously as possible, while making a good faith effort to assist high-speed boaters to 

find an alternative location where this use can be relocated off of the Refuge. 

Determination (check one below): 

 _____ Use is Not Compatible

 X Use is Compatible with the Following Stipulations

Stipulations Necessary to Ensure Compatibility: 

To allow visitor access to the Refuge for wildlife observation and photography, the following 

measurers would be taken:

• By 2008, interpretive signs and an orientation kiosk will be installed on the Headquarters 

Unit of the Refuge to inform visitors about Refuge habitats and wildlife and how to 

minimize adverse impacts. Access to the Refuge will be allowed only between sunrise and 

sunset, unless a permit for alternative hours is issued by the Refuge Manager in advance. 

• The main kiosks on the Headquarters Unit and South Stone Lake units will clearly state 

the regulations governing wildlife observation and photography on the Refuge and will 

include the following information:

(1) a trail map, trail information and regulations;

(2) a description of the National Wildlife Refuge System; and
Stone Lakes NWR Comprehensive Conservation Plan 117

(3) an interchangeable sign for any closures during the waterfowl hunting or Swainson’s 

hawk nesting seasons.

• Trails will be well marked and symbolic fencing will be installed to guide visitor access 

through sensitive habitats. This will minimize trespass into closed areas and reduce 

disturbance to nesting birds and other sensitive species.

• The Refuge will maintain an active law enforcement presence to ensure visitor compliance 

with all Refuge rules and regulations. Refuge law enforcement and other Refuge staff 

presence will be increased to ensure compliance with Refuge regulations.

Justification: The National Wildlife Refuge System Improvement Act of 1997 identifies 

wildlife observation and wildlife photography as priority visitor uses for national wildlife 

refuges, along with hunting, fishing, environmental education and interpretation. In Refuge 

planning and management, priority uses take precedence over other potential visitor uses. 

The Service strives to provide priority visitor uses when compatible with the purpose(s) and 

goals of the Refuge and the mission of the National Wildlife Refuge System (System). 

Expanding existing wildlife observation and photography opportunities on the Refuge 

would allow visitors to experience, enjoy, and learn about native wildlife and plant species in 

the Central Valley. The Refuge has one of the few remaining natural riparian areas in the 

valley as well as wetlands, vernal pools, and open water habitats harboring many species 

of migratory waterfowl, raptors and other wildlife species. Due to its proximity to urban 

areas, the Refuge attracts a high number of visitors. With management consistent with the 

stipulations herein, expanding wildlife observation and photography opportunities would 

substantially increase visitor use and would be compatible with Refuge purposes and the 

System mission. 

Mandatory Reevaluation Date (provide month and year):

 February, 2022 Mandatory 15-year Reevaluation Date (for priority visitor uses)

________Mandatory 10-Year Reevaluation Date (for all uses other than priority visitor uses)

NEPA Compliance for Refuge Use Decision (check one below):

Conducted with Comprehensive Conservation Plan

______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

References Cited:

Cole, D. N. and P. B. Landres. 1995. Indirect effects of recreation on wildlife. Pages 183-201 

in R. L. 

Cole, D. N. and J. L. Marion. 1988. Recreation impacts in some riparian forests of the 
118 Stone Lakes NWR Comprehensive Conservation Plan

eastern United States. Env.Manage. 12:99-107.

Dobb, E. 1998. Reality check: the debate behind the lens. Audubon: Jan.-Feb.

Klein, M. L. 1993. Waterbird behavioral responses to human disturbances. Wildl. Soc. Bull. 

21:31-39.

Liddle, M. J. 1975. A selective review of the ecological effects on human trampling on 

natural ecosystems. Biol.Conserv. 7:17-36.

Morton, J. M. 1995. Management of human disturbance and its effects on waterfowl. Pages 

F59-F86 in W. R.

U.S. Fish and Wildlife Service (USFWS). 2006. Stone Lakes National Wildlife Refuge 

Draft Comprehensive Conservation Plan and Environmental Assessment, 2006. U. S. 

Fish and Wildlife Service, Sacramento, California.

 
Stone Lakes NWR Comprehensive Conservation Plan 119

Compatibility Determination for Environmental Education and Interpretation on the 

Stone Lakes National Wildlife Refuge

Use: Environmental Education and Interpretation

Refuge Name:

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s): 

Stone Lakes NWR purposes include:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. § 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. § 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. § 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. § 715d (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. § 1534 (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).

Description of Use(s):

 Environmental education and interpretation are two of the six priority public uses (e.g., 

hunting, fishing, wildlife observation and photography, environmental educations and 
120 Stone Lakes NWR Comprehensive Conservation Plan

interpretation) identified in the National Wildlife Refuge System Improvement Act of 

1997. Stone Lakes National Wildlife Refuge (Refuge) is one of the few urban refuges in 

the western region and has the potential to attract thousands of visitors annually from 

the greater Sacramento area to experience Central Valley habitats including wetlands, 

grasslands and riparian habitats. Currently, public access to the Refuge is limited to two 

days per month and as a result expectations of the visiting public are not being addressed. 

The Refuge proposes to provide for expanded environmental educational use by: (1)offering 

staff and/or docent led tours on the Refuge,( 2) conducting teacher workshops, (3) 

developing a class or group staging area, (4) developing a Refuge relevant elementary school 

curriculum, and (5) exploring the feasibility of a Refuge fee demonstration area. 

The Refuge plans to develop an interpretive program by: (1) developing a self-guided trail 

system, (2) developing interpretive panels and exhibits, and (3) by building an open air 

interpretive shelter on the Headquarters Unit as part of the Blue Heron Trails project. In 

addition, the Refuge would develop environmental education and interpretive materials, 

including fact sheets on particular species and habitats, and an education guide for educators 

on Central Valley habitat conservation and restoration issues. Additional information about 

this proposed use are in the Stone Lakes National Wildlife Refuge Draft Comprehensive 

Conservation Plan (USFWS, 2006) which is herein incorporated by reference.

Availability of Resources: Staff necessary to oversee the Refuge Environmental 

Education and Interpretation program will be shared with other programs as described 

in the 2006 Draft CCP for Stone Lakes NWR. Additional staff will be required to fully 

implement this program, such as an Interpretative Specialist. Facilities and materials to 

support the program will require capital outlays and recurring costs, however, some of the 

costs will be shared with other visitor programs. If unanticipated costs arise, the program 

will be reevaluated and necessary adjustments made, such as securing additional volunteers 

or financial assistance. 

Item One Time Cost Recurring Costs

Interpretive Panels $210,000 $15,000

Kiosks (1 main + 4 small) $300,000 $5,000

Trails* $1,630,000 $10,000

Outdoor Rec Planner $50,000 $50,000

Maintenance Staff $26,000 $26,000

Administration $2,000 $2,000

Total $2,118,000 $108,000 

*Includes “Junior Biologist Trail” at Headquarters Unit, complete with entrance signs, 

universally accessible trails, entrance kiosk, and interpretive panels. 

Contingent on increased funding and staff identified in the CCP, the Refuge would expand 

interpretation and environmental education opportunities, as well as generate additional 

educational materials. 

Anticipated Impacts of the Use(s): 

Disturbances to wildlife resulting from environmental education and interpretation activities 

are considered to be of minimal impact because: (1) the total number of students permitted 

through the reservation system will be limited, (2) students and teachers will be trained 

in trail etiquette and how to minimize wildlife disturbance, (3) educational groups will 

be required to have a sufficient adult to student ratio for adequate supervision, (4) trail 

design will provide adequate cover for wildlife, and (5) observation areas and scopes will be 

provided to view wildlife at a distance
Stone Lakes NWR Comprehensive Conservation Plan 121

Human activity may disturb migratory birds utilizing Refuge habitats for feeding or nesting 

activities. Off-trail human activity in habitat restoration areas can slow restoration efforts 

through soil compaction, vegetation trampling, and the introduction of invasive plants . 

Litter discarded by visitors can entangle wildlife or be ingested, resulting in injury or death. 

The construction and maintenance of trails and boardwalks will impact soils, vegetation and 

in some instances hydrology around the trails. This could include an increased potential for 

erosion, soil compaction (Liddle 1975), reduced seed emergence (Cole and Landres 1995), 

alteration of vegetative structure and composition and sediment loading (Cole and Marion 

1988).

Federally-listed species that may occur on the Refuge include the giant garter snake, valley 

elderberry longhorn beetle, vernal pool tadpole and fairy shrimp. . No significant impacts 

to vernal pool species are anticipated from environmental education and interpretation 

as visitors to vernal pools areas (e.g., Wetland Preserve) will be confined to established 

trails or led by docents or Refuge staff. California-listed species that inhabit the Refuge 

include greater sandhill crane and Swainson’s hawk. The primary disturbance season for 

Swainson’s hawk is during the nesting season, typically mid-February through July. Prime 

nesting habitat would be closed to visitors during the nesting season. Impacts are also 

discussed in Chapter 5 of the Stone Lakes National Wildlife Refuge Draft Comprehensive 

Conservation Plan (USFWS, 2006).

Public Review and Comment: One comment suggested that educational materials should 

be developed and employed to define and promote low-impact styles of recreation for the 

wildlife resources present. 

Response: The Refuge agrees and content related to environmentally-friendly recreation 

already is and will continue to be a part of the educational programs proposed for the Refuge 

in the CCP.

Determination (check one below): 

_____ Use is Not Compatible

 X Use is Compatible with the Following Stipulations

Stipulations Necessary to Ensure Compatibility: In order to allow public access to 

the Refuge for environmental education and interpretation, the following measurers will be 

taken:

• Access to the Refuge will be allowed only during daylight hours unless a permit for 

alternative hours is issued by the Refuge manager. The Refuge manager will have the 

authority to close certain areas to interpretive programs or to cancel activities to fulfill 

Refuge purposes.

• Public access will be restricted to areas where the least disruption to wildlife and their 

habitats would occur. Visitors will be directed to remain a safe distance from nesting areas 

with signs and barriers. Visitors will be directed away from areas where sensitive habitat 

restoration projects are underway 

• Educators or groups who wish to visit or learn about the Refuge would receive 

interpretive materials in advance. 

• Trails from parking lots to viewing areas will be well marked to minimize trespass through 

closed areas and reduce disturbance to nesting migratory birds and other sensitive 

resources.
122 Stone Lakes NWR Comprehensive Conservation Plan

• The Refuge will maintain an adequate law enforcement capability to ensure public safety 

and compliance with all rules and regulations. 

 Justification:

The goals of the National Wildlife Refuge System (System) include providing an 

understanding and appreciation of fish and wildlife ecology and the human role in the 

environment and providing Refuge visitors with high quality and safe recreational 

experiences oriented toward wildlife, to the extent that these activities are compatible with 

the purposes for which a refuge was established and the mission of the System. Moreover, 

the National Wildlife Refuge System Improvement Act of 1997 identifies environmental 

education and interpretation as priority public uses for National Wildlife Refuges, along 

with hunting, fishing, wildlife observation and photography. As expressed priority uses of 

the Refuge system, these uses take precedence over other potential public uses in Refuge 

planning and management. The Service strives to provide priority public uses when 

compatible with the purpose and goals of the Refuge and the mission of the System. 

Environmental education and interpretive programs provide opportunities for the visiting 

public to learn about and experience native plants, fish and wildlife in their natural habitat. 

The Refuge can also educate the public about its role within the agency and the National 

Wildlife Refuge System, developing better community awareness, volunteer involvement 

and advocacy. The Refuge also has the opportunity to provide the community educational 

information on habitat restoration, migratory waterfowl and wetland conservation in the 

Central Valley. 

Mandatory Reevaluation Date (provide month and year):

 February, 2022 Mandatory 15-year Reevaluation Date (for priority public uses)

________Mandatory 10-Year Reevaluation Date (for all uses other than priority public uses)

NEPA Compliance for Refuge Use Decision (check one below):

Conducted with Comprehensive Conservation Plan

______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

References Cited:

Cole, D. N. and P. B. Landres. 1995. Indirect effects of recreation on wildlife. Pages 183-201 

in R. L. 

Cole, D. N. and J. L. Marion. 1988. Recreation impacts in some riparian forests of the 

eastern United States. Env. Manage. 12:99-107.

Liddle, M. J. 1975. A selective review of the ecological effects on human trampling on 

natural ecosystems. Biol.Conserv. 7:17-36.

 U.S. Fish and Wildlife Service (USFWS). 2006. Stone Lakes National Wildlife Refuge 

Draft Comprehensive Conservation Plan and Environmental Assessment, 2006. U. S. 
Stone Lakes NWR Comprehensive Conservation Plan 123

Fish and Wildlife Service, Sacramento, California.
124 Stone Lakes NWR Comprehensive Conservation Plan

Compatibility Determination for High-Speed Boating on the Stone Lakes National 

Wildlife Refuge

Use: High-Speed Boating

Refuge Name:

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s):

Stone Lakes NWR purposes include:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. “ 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. “ 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. “ 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. “ 715d (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. “ 1534 (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).

Description of Use: 

High-speed boating, primarily associated with waterskiing, has occurred on Refuge 

waterways since before lands and waterways were incorporated into the National Wildlife 
Stone Lakes NWR Comprehensive Conservation Plan 125

Refuge System as part of Stone Lakes NWR. Most of the high-speed boaters are members 

of a private club, Beach Lake Ski Club, who launch power boats from privately-owned 

land within the approved Refuge boundary. Approximately 85 percent of the 2.6 miles 

of waterway used for waterskiing lies within Stone Lakes NWR in the Beach Lake and 

North Stone Lake units. The waterway consists of portions of Lower Beach Lake and 

Southern Pacific Railroad (SP) Cut and is bounded to the west by the abandoned railroad 

levee and primarily by Refuge lands to the east. Most of the channel is relatively narrow, 

approximately 200 to 250 feet across but it expands to approximately 750 feet at its widest 

point. Boaters first pass through 0.47 miles of a privately-owned portion of SP Cut. The 

remainder of the waterski route lies in 1.0 mile of water owned in fee title by the Refuge and 

1.2 miles owned by the state of California and managed by the Refuge under cooperative 

agreement (see Figure 1).

Standard waterskiing, slalom, wake board, and barefoot waterskiing all occur on Refuge 

waters. Boats travel up to 45 mph for barefoot waterskiing (American Barefoot Club 2005) 

and up to 35 mph for slalom waterskiing (USA Waterskiing 2005). Waterskiers modify 

Refuge aquatic habitat by removing floating and submerged woody snags and debris 

presenting a navigational and/or safety hazard and by anchoring a slalom course marked by 

floats and a covered float for docking boats. 

Availability of Resources: No additional funding required.

Anticipated Impacts of Use:

Riparian habitat adjacent to Lower Beach Lake and SP Cut on the Beach and North Stone 

Lake units provides crucial foraging, resting, and breeding habitat for wide variety of 

migratory songbirds, raptors, and waterbirds including waterfowl, waders, and shorebirds. 

Raptors such as the California Endangered Species Act listed Swainson’s hawk, red-tailed 

hawk, red-shouldered hawk, and white-tailed kite and colonially-nesting species such as 

great blue heron, great egret, black-crowned night-heron, snowy egret, and double-crested 

cormorant, may all nest in the woody riparian habitat adjacent to Refuge waterways 

and may be affected by high-speed boating. Though motorized boats generally have a 

greater effect on wildlife, even non-motorized boat use can alter use patterns, reduce use 

of particular habitats, alter feeding behavior and nutritional status, and cause premature 

departure by migratory birds from areas (Knight and Cole 1995). In England, an increased 

rate of disturbance from boats partly caused a decline in roosting numbers of shorebird 

species (Burton et al. 1996). In addition, boaters have been observed to cause massive flights 

of diving ducks on the Mississippi River (Thornburg 1973). Motorized boats within 100 

meters of shore caused all wintering waterfowl and shorebirds to flush between the craft 

and shore in south San Diego Bay, regardless of speed (Huffman 1999). Bow wakes of power 

boats have been reported to tip over free-floating grebe nests as well as other nests near 

the fringe of reeds (Reichholf 1976). However, disturbance to birds, in general, was reduced 

when boats traveled at or below the 5 mph speed limit (Huffman 1999).

The visitor use program proposed in the Comprehensive Conservation Plan (CCP) for 

Stone Lakes NWR (USFWS 2006) includes wildlife viewing and fishing from non-motorized 

boats in the South Stone Lake, Beach Lake, and North Stone Lake units, including the 

same portion of the Refuge currently utilized for waterskiing (Beach Lake and North Stone 

Lake units). High-speed boating will likely not be feasible alongside non-motorized boaters 

because wakes created while traveling at high speed may represent a significant safety 

risk to non-motorized boaters (American Canoe Association 2004). Wakes generated by 

high-speed boaters within SP Cut’s narrow, shallow channel cannot readily dissipate and 

increase in height and steepness as they pass over the shallow nearshore zone that kayakers 

and canoeists are likely to frequent. Even in cases where high-speed boat wakes do not 

actually capsize smaller, non-motorized boats, the waves can create instability sufficient to 
126 Stone Lakes NWR Comprehensive Conservation Plan

discourage other boaters using the channel and diminish their experience of the Refuge (C. 

Courtright, USFWS, pers. comm.). Boats traveling at high speeds in the narrow channel 

could experience difficulty in ceding the right of way to smaller vessels because they may 

lack space in which to give an adequate berth to other boats. In order to drive responsibly, 

previous studies have indicated that waterskiing boats should allow a safety area of 100 

feet on either side of the boat (Bostian 2005. USCG 2006). Where Refuge channels are less 

than 250 feet wide, a high-speed boat would not be expected to be able to safely share the 

waterway with non-motorized craft.

Opportunities for wildlife observation and photography the Refuge proposes to offer visitors 

on waterways in the Beach and North Stone Lake units would also be negatively impacted 

by waterskiing because the noise and speed associated with high-speed boating disturbs 

and displaces wildlife. Moreover, visitors to wildlife refuges and natural areas typically 

seek a natural experience and their wildlife observation experience would be diminished by 

noise. Previous monitoring has indicated that non-motorized boaters find power boats to be 

obtrusive and disruptive of their experience (Pinto, A. 2002).

Wakes generated by power boats are also known to cause levee erosion (U.S. Army Corps 

of Engineers 1997). In non-flow dominated channels, such as SP Cut, boat-generated 

waves exert the greatest erosive energy against levee banks (Ellis 2002). As a result, 

concerns have been expressed regarding wakes generated by motorized boats in SP Cut 

causing significant erosion to the abandoned railroad levee which provides flood protection 

to Reclamation District 744 (Van Loben Sels 2005, Baxter 2005). Continued high-speed 

boat traffic could lead to the need for extensive levee repair or even levee failure. Moreover, 

erosion of the SP Cut levee has resulted in the undermining and toppling of mature riparian 

trees such as valley oaks, eliminating habitat for an array of wildlife species. Therefore, a 

no-wake speed limit is warranted to ensure a quality experience for visitors engaging in 

wildlife-dependent uses, reduce levee erosion, and prevent further loss of property and 

wildlife habitat.

As part of engaging in high-speed boating within Refuge waters, members of the waterski 

club periodically remove navigational hazards that may constitute valuable wildlife habitat. 

These hazards consist largely of submerged snags and floating woody debris which, while 

hazardous for motorized, high-speed boats, provide valuable basking habitat for western 

pond turtles (a State and Federal species of concern). In addition submerged snags and 

floating woody debris provide cover and foraging areas for fish and other wildlife. 

Western pond turtle populations are declining throughout most of their range, particularly 

in Southern California, and the major cause of the decline appears to be the destruction 

of suitable habitat (Brattstrom 1988, Brattstrom and Messer 1988). The only extensive 

populations of turtles currently occur in Northern California and Southern Oregon. Despite 

its name, the western pond turtle is only rarely a pond dweller and prefers the deep, slowflowing waters of sloughs or pools in rivers (Brury 1986). The quiet waters of SP Cut and 

Lower Beach Lake are ideal pond turtle habitat. Moreover, recent graduate studies have 

confirmed that successful nesting by western pond turtles has occurred in tributaries of 

Lower Beach Lake (S. Oliver, pers. comm.). Other components of optimal turtle habitat 

include emergent basking sites, emergent vegetation, mud, rocks and logs (Holland 1992). 

Research conducted on the Trinity River suggests that the preservation and restoration 

of structural features, such as underwater cover and emergent basking sites, is of prime 

importance for promoting pond turtle survival (Reese 1998). Removal of snags and floating 

woody debris for navigational safety purposes degrades the quality of the riparian habitat 

and is therefore not consistent with Stone Lakes NWR purposes or the National Wildlife 

Refuge System mission. 
Stone Lakes NWR Comprehensive Conservation Plan 127

Public Review and Comment: One written and several oral comments recommended that 

high speed boating, associated with water skiing, should be allowed to phase out over a 7 

year period, ending in 2013. Many written and oral comments recommended that high speed 

boating should be eliminated from the Refuge as soon as possible.

Response: High-speed boating was found to be not compatible through this Compatibility 

Determination. According to the compatibility policy (part 603 FW 2, 2.14) “Existing 

uses determined to be not compatible will be expeditiously terminated...this process of 

termination...will not exceed 6 months (without written authorization from the Director)..." 

The Refuge will follow the Service compatibility policy and eliminate high speed boating as 

expeditiously as possible, while making a good faith effort to assist high-speed boaters to 

find an alternative location where this use can be relocated off of the Refuge. 

Determination:

 X Use is Not Compatible

Use is Compatible with the Following Stipulations

Stipulations necessary to ensure compatibility: Not applicable.

Justification: 

High-speed boating is not a wildlife-dependent recreational public use. In light of its 

adverse effects on Refuge natural resources and its affect on the ability of Refuge visitors 

to engage in wildlife-dependent uses, high-speed boating should not be allowed on Refuge 

waters. Instead, it is proposed that a no-wake speed limit be enforced for the following 

reasons:

1) High-speed boaters present a safety risk to non-motorized boaters within the narrow 

confines of this waterway. 

2) High-speed boating disturbs and displaces wildlife because of noise and wake. 

3) Wave action from high-speed boating, in narrow waterways, erodes shorelines and levees 

and causes loss of woody riparian habitat. 

4) High-speed boating may adversely affect wildlife-dependent visitor uses and noise 

associated with high-speed boating may also directly impact visitors.

5) High-speed boating within Refuge waters necessitates removal of navigational hazards 

that constitute valuable habitat for special status species and other fish and wildlife. 

Refuge staff will cooperate with high-speed boaters to seek alternative sites for waterskiing 

outside of the approved Refuge boundary. Other waterskiing sites are available outside the 

approved Refuge boundary that do not have significant adverse effects on visitors to the 

Refuge, wildlife and their habitats, or levee integrity.

Mandatory Reevaluation Date (provide month and year): N/A.

_________ Mandatory 15-Year Reevaluation Date (for priority public uses)

_________ Mandatory 10-Year Reevaluation Date (for all uses other than priority public uses)

NEPA Compliance for Refuge Use Decision (check one below):

______Conducted with Comprehensive Conservation Plan
128 Stone Lakes NWR Comprehensive Conservation Plan

______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

References Cited:

American Barefoot Club. 2005. 2002 ABC Rulebook. http://barefoot.org/documents/

2002ABCRuleBook.PDF

American Canoe Association. 2004. Critical Judgment II: Understanding and Preventing 

Canoe and Kayak Fatalities. 1996-2002.

Baxter, R. D. 2005. Letter to Stone Lakes National Wildlife Refuge, U.S. Fish and Wildlife 

Service. California Department of Parks and Recreation. Sacramento, California.

Bostian, Julie. About.com Waterskiing/Wakeboarding. How to Drive a Boat and Ski 

Responsibly in Traffic. http://waterski.about.com/cs/driverscorner/ht/DriveRespons.

html

Brattstrom, B.H. 1988. Habitat destruction on California with special reference to Clemmys 

marmorata: a perspective. pp. 13-24. In: H. F. DeLisle, P. R. Brown, B. Kaufman and 

B. M. McGurty (eds.). Proceedings of the Conference on California Herpetology. 

Southwestern Herpetological Society, Van Nuys, California. 

Brattstrom, B.H. and D.F. Messer. 1988. Current status of the southwestern pond turtle, 

Clemmys marmorata pallida, in southern California. Final Report for California 

Department of Fish and Game, Contract C-2044. 47 pp. + xii. 

Bury, R.B. 1986a. Feeding ecology of the turtle, Clemmys marmorata. J. Herpetol. 20(4): 

515-521.

Burton, N.H.K., P.R. Evans, and M.A. Robinson. 1996. Effects on shorebird numbers 

of disturbance, the loss of a roost site and its replacement by an artificial island at 

Harlepool, Cleveland. Biol. Conserv. 77:193-201.

Ellis, J.T., D.J. Sherman, B.O. Bauer, and J. Hart. 2002. Assessing the Impact of an Organic 

Restoration Structure on Boat Wake Energy. Journal of Coastal Research. 36:256-265

Holland, D. C. 1991. Distribution and current status of the western pond turtle (Clemmys 

marmorata) in Oregon. Report to the Oregon Department of Fish and Wildlife.

Huffman, K. 1999. San Diego South Bay survey report-effects of human activity and water 

craft on wintering birds in South San Diego Bay. USFWS report.

Pinto, A. 2002. A case study of the nature of conflict between boaters on the lower Salmon 

River in Idaho. Master’s Thesis. The University of Idaho. May 2002.
Stone Lakes NWR Comprehensive Conservation Plan 129

Kahlert, J. 1994. Effects of human disturbance on broods of red-breasted mergansers 

Mergus serrator. Wildfowl 15:222-231.

Knight, R.L. and D.N. Cole. 1995. Wildlife responses to recreationists. in Wildlife and 

Recreationists R.L. Knight and K.J. Gutzwiller, eds.). Island Press, Covelo, California.

Reese, D.A. and H.H. Welsh. 1998a. Habitat use by western pond turtles in the Trinity

river, California. Journal of Wildlife Management. 62(3): 842-853.

Reichholf, J. 1976. The influence of recreational activities on waterfowl. Pages 364-369 in 

M. Smart, ed. Proceedings of the International Conference on the Conservation of 

Wetlands and Waterfowl, Heiligenhafen, Federal Republic of Germany, 2-6 December 

1974. Slimbridger, England: International Waterfowl Research Bureau.

Thornburg, D.D. 1973. Diving duck movements on Keokuk Pool, Mississippi River. J. Wildl. 

Manage. 37:382-389.

USA Water Ski. 2005. American Water Ski Association, Official Tournament Rules. 2005

http://www.usawaterski.org/pages/divisions/3event/2005AWSARulebook.pdf

U.S. Army Corps of Engineers. 1997. Draft Project Modification Report Prospect Island. 

Sacramento, California.

U.S. Fish and Wildlife Service (USFWS). 2006. Stone Lakes National Wildlife Refuge 

Draft Comprehensive Conservation Plan and Environmental Assessment. U. S. Fish 

and Wildlife Service, Sacramento, California.

Van Loben Sels, R. 2005. Letter to the US Fish and Wildlife Service. Reclamation District 

#744 Sacramento, California.

Personal Communications

Clay Courtright, US Fish and Wildlife Service, Sacramento, California, June 4, 2003.
130 Stone Lakes NWR Comprehensive Conservation Plan

Compatibility Determination for Recreational Boating on the Stone Lakes National 

Wildlife Refuge

Use: Recreational Boating Associated with Hunting, Fishing, Wildlife Observation, and 

Photography 

Refuge Name:

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s):

Stone Lakes NWR purposes include the following. 

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” (Emergency Wetlands Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.’ (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: 

“The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).

Description of Use: 
Stone Lakes NWR Comprehensive Conservation Plan 131

The visitor use program proposed in the Comprehensive Conservation Plan (CCP) for 

Stone Lakes NWR (USFWS 2006a) includes recreational boating that supports priority 

visitor uses, including hunting, fishing, wildlife observation, photography, environmental 

education, and interpretation. The recreational boating uses addressed in this compatibility 

determination consist of car-top, hand-launched boats, such as kayaks and canoes and boats 

with electric motors, with some restrictions. 

Regulation of recreational boating on the Refuge will be managed to minimize safety risks, 

as well as adverse effects on wildlife, habitat, and other recreational users, particularly those 

engaged in wildlife-dependent uses. These restrictions will include a no-wake speed limit 

throughout Refuge waters, seasonal closures, and limitations on use of electric motors. No 

gas-powered outboard motors will be permitted. The no-wake zone is intended to protect 

non-motorized boaters, wildlife and wildlife habitat. The restrictions are also intended to 

protect levees from deterioration by wave action (Baxter 2005, Van Loben Sels 2005) and to 

reduce noise levels that could adversely affect wildlife. 

Waterways open to boating will include South Stone Lake, Southern Pacific Railroad (SP) 

Cut, and Lower Beach Lake. Boat launch, access, and parking for Lower Beach Lake and 

SP Cut on the Beach Lake Unit will be from the west end of Elliott Ranch Road. Current 

facilities are limited to a gravel parking area and an unimproved boat launch. Parking 

approximately 10 cars and an improved boat launch will be constructed at Elliot Ranch 

Road, contingent upon available funding. The second boat launch site is on the Sun River 

property of the South Stone Lake Unit where parking will be expanded to accommodate 

approximately 20 cars. Depending on availability of staff and funding, a new boat haul-out 

and associated trail and observation blind will be provided at the Lodi Gun club property of 

the South Stone Lake Unit to be accessible only by boat. 

All Refuge waterways will be open for recreational boating from June through September 

only. Waterways will be closed to recreational boating for October 1 through May 31, to 

minimize disturbance to nesting waterbirds and raptors such as herons, egrets, grebes, 

and Swainson’s hawks. Waterways being treated for invasive aquatic weeds (e.g., water 

hyacinth, Egeria densa) will be closed to boating during herbicide applications. Temporary 

closures to boating may also be required during particular habitat restoration or 

management projects. Private vendors wishing to lead boating groups will be required to 

apply for a Refuge Special Use Permit. Chapter 5 of the Comprehensive Conservation Plan, 

Refuge Vision, Goals and Objectives, are herein incorporated by reference. 

Availability of Resources:

The following funding/annual costs would be required to administer and manage boating 

activities as described above:

Activity One-time Costs Recurring Costs

Improvement of boat ramp and parking LOT $30,000

Maintenance of Parking Lots and Boat Launches $5,000

Maintenance (0.50 FTE) $26,000 $26,000

Law Enforcement (0.5 FTE) $25,000 $25,000

Install Signs (includes all public use signs) $10,000

Maintain Signs $5,000

Administration $2,000 $2,000

TOTAL $93,000 $63,000

Funding will be sought through the Service budget process. Other opportunities may 
132 Stone Lakes NWR Comprehensive Conservation Plan

include: expanded partnerships with the State and recreational user groups, grants, 

coordination with other law enforcement agencies, and additional Refuge operations. All 

funding will be utilized to support a safe, quality public use program as described above. 

Anticipated Impacts of Use:

Stone Lakes NWR provides crucial foraging and breeding habitat for wintering migratory 

birds, including waterfowl, shorebirds, and other waterbirds. Great blue herons, great 

egrets, double-crested cormorants, and Swainson’s hawks, in particular, may be affected 

by recreational boating since they nest in tall riparian trees adjacent to waterways used 

by boaters. Though motorized boats generally have a greater effect on wildlife, even nonmotorized boat use can alter distribution, reduce use of particular habitats by waterfowl and 

other birds, alter feeding behavior and nutritional status, and cause premature departure 

from areas (Knight and Cole 1995). In the Ozark National Scenic Riverway, green heron 

activity declined on survey routes when canoes and boat use increased on the main river 

channel (Kaiser and Fritzell 1984). Canoes or slow moving boats have also been observed 

to disturb nesting great blue herons (Vos et al. 1985). However, compared to motorboats, 

canoes and kayaks appear to have less disturbance effects on most wildlife species (Jahn and 

Hunt 1964, Huffman 1999, DeLong 2002) and disturbance to birds, in general, is reduced 

when boats travel at or below the 5 mph speed limit (Huffman 1999). To protect waterbirds 

and raptors that nest in riparian trees, the Beach Lake and South Stone Lake units will 

be closed to recreational boating from October through May, during nesting and breeding 

seasons. Monitoring of nesting great blue herons, Swainson’s hawks and other waterbirds 

will be periodically conducted to assess the impact of recreational boating use. 

Federally-listed species that may occur on the Refuge include the giant garter snake, valley 

elderberry longhorn beetle, vernal pool tadpole, and vernal pool fairy shrimp (USFWS 

2006b). No effects on the beetle or vernal pool species are anticipated because recreational 

boating will occur outside of the habitats of these species. However, giant garter snakes 

could be affected by vehicular use of the area if they happen to be crossing a roadway. 

Vehicular speed limits will therefore be enforced within the Refuge to reduce effects to 

wildlife. 

Western pond turtle populations are declining throughout most of their range, particularly 

in Southern California, and the major cause of the decline appears to be the destruction of 

suitable habitat (Brattstrom 1988, Brattstrom and Messer 1988). Because of its precipitous 

decline in numbers, the Western pond turtle has been designated as a Federal and State 

species of concern. The only extensive populations of turtles currently occur in Northern 

California and Southern Oregon. Despite its name, the western pond turtle is only rarely a 

pond dweller and prefers the deep, slow-flowing waters of sloughs or pools in rivers (Brury 

1986). The quiet waters of the Beach Lake and South Stone Lake units are ideal pond turtle 

habitat. Recent graduate studies have confirmed that western pond turtles successfully 

nest on the Refuge (S. Oliver, pers. comm.). Other components of optimal turtle habitat 

include emergent basking sites, emergent vegetation, mud, rocks, and logs (Holland 1992). 

Research conducted on the Trinity River suggests that the preservation and restoration 

of structural features, such as underwater cover and emergent basking sites, is of prime 

importance for promoting pond turtle survival (Reese 1998). To occur safely, high-speed 

boating necessitates removal of snags and other underwater hazards that also provide 

valuable turtle habitat. However, no such alteration of habitat is necessary to provide nowake boating opportunities. Nevertheless, canoes, kayaks, and car-top boats with electrical 

motors can still be expected to have some disturbance effect on turtles by displacing them 

from basking sites.
Stone Lakes NWR Comprehensive Conservation Plan 133

Public Review and Comment: Several written comments recommended that the Refuge 

be opened to paddle boat (canoe, kayak, etc.) recreation.

Response: The Refuge intends to open the SP cut waterway on the Refuge, from the west 

end of Elliott Ranch Road southward, to car top boating beginning in 2008.

Determination:

______ Use is Not Compatible

 X Use is Compatible with the Following Stipulations

Stipulations necessary to ensure compatibility:

The following stipulations are required to ensure that recreational boating is compatible:

• A no-wake speed limit will be implemented throughout Refuge waters. Only humanpowered canoes and kayaks, and electric-powered car-top boats (that is, non-trailered 

boats which can be carried on top of, inside of, or in the back of a vehicle and can be handlaunched into the water) will be permitted throughout Refuge waters.

• A seasonal closure from October through May will be implemented to reduce disturbance 

to wintering, nesting, resting, foraging, and breeding birds and other wildlife, their 

habitats, and other recreational users, especially those participating in wildlife-dependent 

visitor uses.

• Removal of snags and floating woody debris for navigational safety purposes will not be 

permitted.

• Signs will be installed and maintained to mark closed areas, convey seasonal closures, and 

indicate no-wake regulations on the Refuge.

• Periodic law enforcement will help ensure compliance with speed limit regulations and area 

closures. Regulations will be described in brochures and posted at Refuge headquarters 

and at boat launch sites. Recreational boaters are required to be in compliance with all 

applicable Refuge, U.S. Coast Guard and State of California regulations and laws.

• Boating activities and associated effects will be monitored with regard to waterfowl, 

shorebirds, birds of prey, other wildlife and their habitats, and other recreational users, 

especially those participating in wildlife-dependent visitor uses. 

• Monitoring data will be used by the Refuge manager in making necessary adjustments 

in regulations or other aspects of the Refuge boating program and in the periodic 

reevaluation of this Compatibility Determination. 

Justification: Boating itself is not wildlife-dependent recreation, but many wildlife 

dependent recreational activities (waterfowl hunting, fishing, wildlife observation, 

photography, and environmental education and interpretation) are associated with boating. 

A carefully regulated boating program would help the Refuge provide opportunities for 

wildlife-dependent priority visitor uses, which would contribute toward fulfilling provisions 

under the National Wildlife Refuge System Administration Act as amended in 1997.

Although boating has a potential to impact wildlife, implementing the prescribed stipulations 

listed above will reduce many of these impacts. Adequate habitat will be available for 
134 Stone Lakes NWR Comprehensive Conservation Plan

wintering and breeding waterfowl, birds of prey, and other wetland-dependent species 

because high wildlife use areas will be closed to boating during critical periods. Boating 

regulations will be maintained and enforced in order to minimize the impact of visitor use 

on wildlife and wildlife habitat. Thus, migratory birds will find sufficient food resources and 

resting places so their abundance and use of the Refuge will not be measurably lessened; 

their physiological condition and production will not be impaired; their behavior and 

normal activity patterns will not be dramatically altered; and their overall status will not be 

impaired. The Refuge will also implement a monitoring program to help assess disturbance 

effects on wildlife and habitat. The impacts associated with boating activities can be reduced 

through improved outreach and educational information for Refuge visitors involved in these 

activities.

Mandatory Reevaluation Date (provide month and year):

 Mandatory 15-Year Reevaluation Date (for priority public uses)

 February, 2017 Mandatory 10-Year Reevaluation Date (for all uses other than priority 

 public uses) 

NEPA Compliance for Refuge Use Decision (check one below):

______ Categorical Exclusion without Environmental Action Statement

______ Categorical Exclusion and Environmental Action Statement

 X CCP Environmental Assessment and Finding of No Significant Impact

______ Environmental Impact Statement and Record of Decision

References Cited:

Baxter, R. D. 2005. Letter to Stone Lakes National Wildlife Refuge, U.S. Fish and Wildlife 

Service. California Department of Parks and Recreation. Sacramento, California.

Brattstrom, B.H. 1988. Habitat destruction on California with special reference to 

Clemmys marmorata: a perspective. Pp. 13-24 In: H. F. DeLisle, P. R. Brown, B. 

Kaufman and B. M. McGurty (eds.). Proceedings of the Conference on California 

Herpetology. Southwestern Herpetological Society, Van Nuys, California. 

Brattstrom, B.H. and D.F. Messer. 1988. Current status of the southwestern pond turtle, 

Clemmys marmorata pallida, in southern California. Final Report for California 

Department of Fish and Game, Contract C-2044. 47 pp. + xii. 

Bury, R.B. 1986a. Feeding ecology of the turtle, Clemmys marmorata. J. Herpetol. 20(4): 

515-521.

Burton, N.H.K., P.R. Evans, and M.A. Robinson. 1996. Effects on shorebird numbers 

of disturbance, the loss of a roost site and its replacement by an artificial island at 

Harlepool, Cleveland. Biol. Conserv. 77:193-201.

DeLong, A. 2002. Managing Visitor Use & Disturbance of Waterbirds. A Literature Review 

of Impacts and Mitigation Measures.
Stone Lakes NWR Comprehensive Conservation Plan 135

Holland, D. C. 1991. Distribution and current status of the western pond turtle (Clemmys 

marmorata) in Oregon. Report to the Oregon Department of Fish and Wildlife.

Huffman, K. 1999. San Diego South Bay survey report-effects of human activity and water 

craft on wintering birds in South San Diego Bay. USFWS report.

Jahn, L.R. and R.A. Hunt. 1964. Duck and coot ecology and management in Wisconsin. 

Wisconsin Conserv. Dep. Tech. Bull. No. 33. 212pp.

Kahlert, J. 1994. Effects of human disturbance on broods of red-breasted mergansers 

Mergus serrator. Wildfowl 15:222-231.

Kaiser, M.S. and E.K. Fritzell. 1984. Effects of river recreationists on green-backed heron 

behavior. J. Wildl. Manage. 48: 561-567.

Knight, R.L. and D.N. Cole. 1995. Wildlife responses to recreationists. in Wildlife and 

Recreationists R.L. Knight and K.J. Gutzwiller, eds.). Island Press, Covelo, California.

Reese, D.A. and H.H. Welsh. 1998a. Habitat use by western pond turtles in the Trinity 

River, California. Journal of Wildlife Management. 62(3): 842-853.

Thornburg, D.D. 1973. Diving duck movements on Keokuk Pool, Mississippi River. J. Wildl. 

Manage. 37:382-389.

U.S. Fish and Wildlife Service (USFWS). 2006a. Stone Lakes National Wildlife Refuge 

Draft Comprehensive Conservation Plan and Environmental Assessment, September 

2005. U. S. Fish and Wildlife Service, Sacramento, California.

U.S. Fish and Wildlife Service (USFWS). 2006b. Biological Opinion for the Stone Lakes 

National Wildlife Refuge Comprehensive Conservation Plan (1-8-01-FW-66). U.S. Fish 

and Wildlife Service, Sacramento, California.

Van Loben Sels, R. 2005. Letter to Stone Lakes National Wildlife Refuge, U.S. Fish and 

Wildlife Service. Reclamation District #744. Sacramento, California.

Vos, D.K., R.A. Ryder, and W.D. Graul. 1985. Response of breeding great blue herons to 

human disturbance in North-central Colorado. Colonial Waterbirds 8:13-22.
136 Stone Lakes NWR Comprehensive Conservation Plan
Stone Lakes NWR Comprehensive Conservation Plan 137

Compatibility Determination for Research on the Stone Lakes National Wildlife 

Refuge

Use: Research

Refuge Name:

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s):

Stone Lakes NWR purposes include:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. § 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. § 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. § 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. § 715d (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. § 1534 (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).

Description of Use(s): 

Stone Lakes National Wildlife Refuge (Refuge) periodically reviews proposals for scientific 

research to be conducted on the Refuge or may recommend possible research topics 
138 Stone Lakes NWR Comprehensive Conservation Plan

to professors or students from nearby academic institutions. Although research is not 

identified as a priority public use by the National Wildlife Refuge System Improvement 

Act of 1997, scientific research can benefit Refuge resources and support the purpose of the 

Refuge and mission of the System. The Refuge proposes to give priority to studies that 

contribute to the conservation, enhancement, , management, or use of native Refuge fish and 

wildlife populations and their habitats. Research proposals would be reviewed by Refuge 

staff or other specialists, as appropriate. Research proposals that met the following criteria, 

would be given priority consideration for approval: 

• Research that would contribute to Refuge conservation, enhancement, management, or 

visitor use programs;

• Research that would not conflict with other ongoing management, monitoring, or research 

programs;

• Research that could only be conducted on the Refuge;

• Research that did not result in undue disturbance to Refuge fish and wildlife and their 

habitats; and

• Research that could be monitored by the Refuge within existing staffing or logistical 

constraints.

Availability of Resources: 

Adequate funding and staff exist to manage research at the Stone Lakes NWR. . 

Anticipated Impacts of the Use(s):

Some level of disturbance is expected from many research activities since they commonly 

occur in areas normally closed to the public and may involve collecting samples or handling 

fish and wildlife. However, minimal impact to Refuge resources would be anticipated since 

research studies would be governed by a Special Use Permit (SUP) annually issued by the 

Refuge. SUP conditions would ensure that impacts to wildlife and habitats are minimized. 

All projects would be reviewed annually to assess compliance with SUP conditions. Prior to 

their approval, research proposals would be evaluated to ensure their study design resulted 

in the least possible level of disturbance to sensitive Refuge resources.

Public Review and Comment: No public comments were received related to research 

occurring on the Refuge.

Determination (check one below): 

_____ Use is Not Compatible

 X Use is Compatible with the Following Stipulations

Stipulations Necessary to Ensure Compatibility: 

Research applicants would be required to submit a proposal summarizing: 

(1) Objectives of the study; 

(2) Justification for the study; 

(3) Description of study methodology and schedule;

(4) Description of potential impacts on Refuge fish and wildlife and/or habitats, including 

short-term and long-term disturbance, injury, or mortality; 

(5) Summary of research personnel required and their qualifications/experience; 

(6) Status of necessary permits (e.g., scientific collecting permits, endangered species 

permit),;
Stone Lakes NWR Comprehensive Conservation Plan 139

(7) Anticipated costs to the Refuge and any requests for Refuge staff assistance; and 

(8) Planned deliverables and end products (e.g., reports, publications). 

If proposed research methods adversely affect or have the potential to adversely affect 

Refuge resources, the researcher will be required to implement mitigation measures to 

minimize potential impacts. Mitigation measures will be included as conditions on the 

Special Use Permit. Refuge staff will monitor and inspect research projects to assess any 

unanticipated environmental effects and will have authority to terminate any research 

project, if necessary. All Refuge rules and regulations will be adhered to by researchers, 

unless specifically waived under a Special Use Permit issued by Refuge management. 

Justification: Well-defined research projects developed in consultation with Service staff, 

would contribute directly to the conservation, enhancement, protection, management, 

and use of native Refuge fish and wildlife populations and their habitats. Adequate SUP 

conditions will be imposed on any research project to ensure that short and long-term 

impacts on Refuge resources are minimized, Only research that is compatible with the 

purposes of the Refuge and mission of the System would be permitted on the Refuge

Mandatory Reevaluation Date (provide month and year):

 Mandatory 15-Year Reevaluation Date (for priority public uses)

February, 2017 Mandatory 10-Year Reevaluation Date (for all uses other than priority 

 public uses)

NEPA Compliance for Refuge Use Decision (check one below):

Conducted with Comprehensive Conservation Plan

______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

References Cited:

U.S. Fish and Wildlife Service (USFWS). 2006. Stone Lakes National Wildlife Refuge 

Draft Comprehensive Conservation Plan and Environmental Assessment, 2006. U. S. 

Fish and Wildlife Service, Sacramento, California.
140 Stone Lakes NWR Comprehensive Conservation Plan
Stone Lakes NWR Comprehensive Conservation Plan 141

Compatibility Determination for Plant Gathering on the Stone Lakes National 

Wildlife Refuge

Use: Plant Gathering

Refuge Name:

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s):

Stone Lakes NWR purposes include:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. § 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. § 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. § 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. § 715d (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. § 1534 (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).

Description of Use(s):

The gathering of plants in and around Stone Lakes National Wildlife Refuge by Native 

Americans occurred historically and continues to be an ongoing use today. Plants are 
142 Stone Lakes NWR Comprehensive Conservation Plan

gathered for a variety of uses; for medicinal uses, ceremonial uses, as food stuffs and for 

utilitarian or artistic purposes such as basket weaving or cord making. Plants gathered for 

traditional uses may include; willow bark and branches (Salix spp.), mugwort (Artemisia 

douglasiana), tule (Schoenoplectus acutus var. occidentalis, syn. Scirpus acutus), Santa 

Barbara sedge (Carex barbarae), wild rose (Rosa californica), indian hemp (Apocynum 

cannabinum), oak acorns (Quercus spp.) and others. Plants are gathered during various 

seasons; acorns, bulbs and berries are gathered in the late summer or fall, while medicinal 

or ceremonial herbs and basketweaving materials may be gathered in spring. The amount 

of plant material being harvested is traditionally low and is not expected to increase. Special 

Use Permits will be issued by the Refuge for plant gathering and access regulated to ensure 

protection of critical habitat during nesting or breeding periods. The use of Refuge lands for 

collections is considered to be of vital importance to Native American cultural groups such as 

the California Indian Basketweavers Association. 

For additional details about this proposed use, please see the Environmental Assessment 

(Appendix B) for the Stone Lakes National Wildlife Refuge Draft Comprehensive 

Conservation Plan (USFWS 2006) which is herein incorporated by reference.

Availability of Resources: No additional resources will be needed to support this use.

Anticipated Impacts of the Use(s):

Impacts are also discussed in the Environmental Assessment (Appendix B) for the Stone 

Lakes National Wildlife Refuge Draft Comprehensive Conservation Plan (USFWS 2006) 

Impacts to habitat and wildlife associated with plant gathering on the Refuge are minimal. 

The amount of plant material being harvested is small enough not to constitute any 

meaningful impact on habitat. The level of disturbance to wildlife will vary depending on 

the season, but is considered to be low overall. The gathering of acorns, berries, bulbs and 

other plant materials that occurs from late summer through fall will have little or no impact 

on migratory or nesting birds. Gathering of new plant growth in springtime, herbs for 

medicinal/ceremonial purposes and willow twigs and bark for basket weaving may coincide 

with use of the refuge by migratory waterfowl, but as gathering activities are limited, impact 

is also expected to be limited. 

Disruptions to Refuge management may occur if routine herbicide applications for invasive 

terrestrial weeds require modification due to plant gathering activities. Refuge staff avoid 

application of herbicides to plants known to be valuable for food, medicinal, ceremonial, and 

ornamental or other cultural uses. However, this adjustment of management practices is 

not considered burdensome and will not adversely affect control of invasive weeds or habitat 

restoration projects.

Federally listed species that may occur on the Refuge include the giant garter snake, 

valley elderberry longhorn beetle, vernal pool tadpole and fairy shrimp. No impacts to 

vernal pool species are anticipated from plant gathering since gathering activities will not 

be occurring on or near the vernal pool Wetland Preserve Unit of the Refuge. State listed 

species that inhabit the refuge include greater sandhill crane and Swainson’s hawk. The 

primary disturbance season for Swainson’s hawk is during the nesting season, typically midFebruary through July. Prime nesting habitat would be closed to visitors during the nesting 

season. 

Public Review and Comment: No public comments were received related to plant 

gathering on the Refuge.

Determination (check one below): 

_____ Use is Not Compatible
Stone Lakes NWR Comprehensive Conservation Plan 143

 X Use is Compatible With Following Stipulations

Stipulations Necessary to Ensure Compatibility: 

In order to accommodate access to the Refuge for plant gathering, the following measurers 

will be taken:

Plant gathering activities will be reviewed as part of annual coordination with tribal 

representatives. If monitoring by the Refuge reveals that impacts from plant gathering 

have increased so the activity is adversely affecting wildlife or habitat, then permitees will 

be required to adjust their activities to avoid impacts. Adjustments may include reductions 

in harvest, changes in timing of gathering, or reductions in numbers of visitors or frequency 

of visitors.

The Refuge manager will have the authority to close areas within the Refuge during 

sensitive wildlife use periods and cancel any collecting activities deemed necessary to fulfill 

Refuge purposes or ensure visitor safety. Sensitive nesting areas will be protected from 

disturbance by visitors with signs and barriers. Visitors will be directed away from areas 

where major habitat restoration or management projects are under way. 

Justification:

One of the goals of the National Wildlife Refuge System (System) is providing the public an 

understanding and appreciation of fish and wildlife ecology, wildlife habitat and the human 

role in the environment. The Service strives to provide priority visitor uses when compatible 

with the purpose and goals of the Refuge and the mission of the System. The National 

Wildlife Refuge System Improvement Act of 1997 identifies environmental education and 

interpretation as priority public uses for National Wildlife Refuges, along with hunting, 

fishing, wildlife observation and photography. Though plant gathering is not a wildlifedependent recreational use, it is an activity that contributes to environmental education and 

awareness. An understanding of plant ecology is essential to successful plant harvesting, 

thus this activity helps to educate participants about Central Valley habitats, while 

sustaining cultural practices.

Mandatory Reevaluation Date (provide month and year):

 Mandatory 15-year Reevaluation Date (for priority public uses)

February, 2017 Mandatory 10-Year Reevaluation Date (for all uses other than priority 

 public uses)

NEPA Compliance for Refuge Use Decision (check one below):

Conducted with Comprehensive Conservation Plan

______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

References Cited:
144 Stone Lakes NWR Comprehensive Conservation Plan

U.S. Fish and Wildlife Service (USFWS). 2006. Stone Lakes National Wildlife Refuge 

Draft Comprehensive Conservation Plan and Environmental Assessment, 2006. U. S. 

Fish and Wildlife Service, Sacramento, California.
Stone Lakes NWR Comprehensive Conservation Plan 145

Compatibility Determination for Mosquito Control on the Stone Lakes National 

Wildlife Refuge

Use: Monitor and Control Mosquitoes

Refuge Name:

Stone Lakes National Wildlife Refuge

Sacramento County, California

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s):

Stone Lakes NWR purposes include:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. § 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. § 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. § 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. § 715d (Migratory Bird Conservation Act)

 “... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. § 1534 (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: 

The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).

Description of Use: 

Stone Lakes National Wildlife Refuge (Refuge) proposes to continue to collaborate with 

Sacramento-Yolo Mosquito Vector Control District (District) in monitoring and controlling 
146 Stone Lakes NWR Comprehensive Conservation Plan

mosquitoes to address the human health concerns of neighboring communities. The Refuge 

is located within Sacramento County, 10 miles south of downtown Sacramento and bordered 

by the city of Elk Grove on the east. The potential for mosquito production in Refuge waters 

is worrisome to residents, and indeed, urbanized areas adjacent to the Refuge are within 

the flying range of many species of mosquitoes. Because of this, Refuge staff and SYMVCD 

(District) entered into a Memorandum of Understanding (MOU) in 1993, to establish a 

framework within which the District may continue to control and abate mosquitoes within 

the Refuge, consistent with the goals and objectives of the Refuge. Both the Refuge and the 

District agree that biological, cultural and physical mosquito control methods are preferred 

over chemical methods and that wetlands can be designed and managed to avoid or 

minimize mosquito breeding. In summary, the MOU provides for: 1) allowing the District to 

comment on planned Refuge wetland projects, 2) providing the District an annual summary 

of planned Refuge water management and notification of flood-ups and irrigations, 3) the 

District providing a proposed annual mosquito abatement operating plan to the Refuge, 

4) the Refuge submitting pesticide use permits (PUP’s) for mosquito control chemicals 

requested by the District, 5) providing access for mosquito monitoring and biological control 

measures such as mosquito fish planting as defined in a Special Use Permit (SUP) and 6) 

with notification and coordination, application of larvicides or adulticides, when specified 

thresholds are exceeded.

Many species of mosquitoes are known vectors of serious diseases in California. Although 

12 mosquito-borne viruses are known to occur in California, only West Nile virus (WNV), 

western equine encephalomyelitis virus (WEE), and St. Louis encephalitis virus (SLE) are 

significant causes of human disease as of 2006 (CDHS 2006). As was learned with the recent 

(2005, 2006) WNV outbreaks, it is possible that new mosquito-borne diseases may cause 

outbreaks in the future. Since, each disease and associated vector has specific biological 

and ecological characteristics, a wide variety of control methods, in accordance with the 

principles of integrated pest management, must be kept available to prevent and respond to 

new outbreaks in a timely manner. WEE tends to be most serious in very young children, 

whereas elderly people are most at risk to SLE and WNV (CDHS 2003). California is also 

at risk for West Nile virus (WNV) which was first detected in the summer of 2003 in adult 

mosquitoes in Imperial County and in crows in Orange County. WNV was detected within 

Sacramento County in 2004, though it has principally affected birds and horses. In 2005, 

West Nile Virus (WNV) became established in Sacramento and Yolo counties, triggering 

aggressive and widespread mosquito control efforts. In August of 2005 the number of 

human WNV cases and rate of infected adult mosquitoes were so high that the District 

conducted aerial applications of pyrethrin over a major portion of Sacramento County 

(Sacramento County 2006). 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 

(CDHS 2003). With the exception of available vaccines to protect horses against WEE and 

WNV, there are no known specific treatments or cures for diseases caused by these viruses 

(CDHS 2003). 

Mosquito control at the Refuge follows an ordered succession, using nonchemical treatments 

first (e.g., water control strategies, vegetation management, mosquitofish, etc.), resorting 

to chemical treatment only when necessary, as determined through standard mosquito 

monitoring procedures. Among chemical treatments, adulticides will be used as a last resort. 

For example, wetlands that have produced large mosquito populations in the past will be 

flooded as quickly as possible to minimize multiple emergencies that may cause a need for 

adulticiding. Refuge staff work closely with the District to reduce or eliminate mosquitoes 

on the refuge by means of biological controls and habitat management. The MOU signed 
Stone Lakes NWR Comprehensive Conservation Plan 147

by the District and the Refuge outlines an effective biological mosquito suppression 

program that includes wetland design, water level management recommendations, research 

partnerships, and the introduction of native and non-native fish that prey on mosquito 

larvae.

The mosquito species identified by SYMVCD for monitoring and control are Culex tarsalis, 

Anopheles freeborni, Aedes vexans, Aedes melanimon, Aedes nigromaculis, and Aedes 

increpitus. Culex tarsalis is the primary vector of WEE and SLE in California and is 

also considered to be a significant vector of WNV (CDHS 2003). Anopheles freeborni can 

transmit the malaria parasite to humans and is common in the rice growing regions of 

California. Aedes melanimon is involved in the encephalitis virus (sleeping sickness) cycle 

and is a severe outdoor pest (SYMVCD 2004). 

Mosquito Monitoring

The District’s monitoring activities are designed to estimate the abundance of immature 

(larvae and pupae) and adult mosquito populations. Monitoring activities that may be 

conducted on the Refuge include, larval sampling, adult light traps and host-seeking traps, 

leg counts, wild bird sera testing and chicken sera testing (off the Refuge). The wild bird 

sera testing is part of an ongoing cooperative program between the District and the Refuge 

to assess populations of resident and migratory songbirds and their role in the transmission 

of disease. 

Monitoring visits by District staff may occur as often as 3-4 times per week during 

the summer irrigation (May 1 - July 31) and fall flood-up (August 1 - October 15). If 

temperatures are above average beyond October 15, District staff may continue to require 

access to the Refuge for additional monitoring. 

Dip counts are used to estimate the numbers of immature mosquitoes and to determine the 

need for mosquito control. The dipper method entails using a long-handled ladle (ca 500 ml) 

called a dipper to collect water samples from pools potentially serving as mosquito sources. 

Captured immature mosquitoes would be identified taxonomically by skilled technicians. All 

Refuge wetland units could potentially be monitored using the dipper method. However, the 

areas of Refuge wetland units that are potential mosquito habitat would be targeted. Target 

areas would include wetland margins, shorelines and riparian areas.

Light and carbon dioxide traps are used to capture adult mosquitoes for monitoring 

purposes. Light traps are cylinders with a light, fan and collecting jar. The mosquitoes are 

attracted to the light and enter the cylinder. The fan creates an air current that moves the 

mosquitoes into the collecting jar. Carbon dioxide (CO2 ) baited traps are used to monitor 

density of adult mosquitoes and to identify adults to species. The trap used is baited with 1-2 

kg (2.2–4.4 lbs.) of dry ice next to the trap. A motor and fan on the three inch diameter trap 

sucks mosquitoes down into a container like a modified gallon ice cream carton with tubular 

surgical stockinet attached to the bottom of the motor housing unit to retain the collected 

mosquitoes. 

As part of monitoring conducted by the District for the presence of these viruses, a sentinel 

chicken flock is maintained in a pen nearby, but not on, Refuge lands. Sentinel chickens are 

exposed to the environment and to mosquitoes moving through the area that may choose to 

feed on them. Regular blood samples are periodically taken from the chickens to detect any 

mosquito-vector pathogen activity.

The monitoring activities described above are conducted under a SUP between the Refuge 

and SYMVCD. The Refuge proposes to allow the SYMVCD to continue these activities 
148 Stone Lakes NWR Comprehensive Conservation Plan

under an annual SUP.

Mosquito Control with larvicides/pupacides: 

The District proposes to control mosquitoes by treating areas infested with larval stages of 

Culex tarsalis; Aedes melanimon, Aedes nigromaculis, Anopheles freeborni and Aedes spp. 

Treatment thresholds as of 2006 were 0.1 mosquito larvae per 350-ml dipper of water for all 

species; however, this may change to respond to changes in mosquito populations, disease 

levels, or other factors that affect public health (Boyce 2005). The District would use the 

biological larvicides Bacillus thuringiensis isrealensis (Bti) and Bacillus sphaericus (Bsp) 

and the insect growth inhibitor methoprene. Use of the petroleum distillate GB1111 as a 

pupacide was discontinued after 2000 and has been replaced with the monomolecular film 

Agnique. These treatments would be applied via ground methods. 

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 binds to protein specific receptors of 

susceptible insect species resulting in the lethal response (Lacey and Mulla 1990). Bti must 

therefore be ingested by the target insect to be effective. It is most effective on younger 

mosquito larval instars but does not affect pupae or adult mosquitoes. The District prefers 

to use Bti because of the low impacts to the environment and non-target organisms and its 

effectiveness in reducing the numbers of target pests. The Bti formulations Vectobac 12AS 

or Vectobac G would be employed at the Refuge by the District.

Like Bti, Bsp is a microbial insect pathogen with a similar mode of action (Walton, 1998). 

Formulated Bsp products used as mosquito larvicides consist of bacterial spores and protein 

endotoxins. The granular formulation of Bsp, Vectolex CG, would be applied by the District. 

Both Bti and Bsp may be applied as a spot treatment to small areas or broadcast over larger 

areas. 

Methoprene is a synthetic insect growth regulator (IGR) 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 

but does not affect pupae or adult mosquitoes (ETN 1996). Treated larvae will pupate, but 

will not emerge as adults. The District proposes to use the insect growth regulators, most 

commonly the formulated methoprene products such as AltosidTM Liquid, AltosidTM Pellets 

and AltosidTM XR-G.

The monomolecular film, Agnique, reduces water surface tension. This interferes with 

larval orientation at the air-water interface and/or increases wetting tracheal surfaces, thus 

suffocating the organism. As the film spreads over the water surface, it tends to concentrate 

mosquito pupae, which may increase mortality from crowding stress (Dale and Hulsman 

1990).

Applications of larvicides may occur anywhere in the wetland and moist soil units of the 

Refuge. The potential wetland areas for mosquito breeding and consequently mosquito 

treatment include managed permanent wetlands (106 acres), irrigated pastures (490 acres) 

and occasionally perennial wetlands (193 acres), totaling approximately 790 acres. The 

shorelines of open water areas may be treated. In addition, the District will treat ditches, 

culverts and low areas not classified as wetlands. 
Stone Lakes NWR Comprehensive Conservation Plan 149

The total area of the Refuge that is treated varies with the conditions of each year. Annual 

precipitation amounts 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. The range in area treated in the last five years varied from a low of 104 acres in 2000 

to a high of 477 acres in 2004. The majority of the treatments occur from August to October, 

but applications of larvicides can begin as early as March and extend into November. 

Mosquito control with adulticides

Treatment thresholds for adult control are based on multiple factors including: date, 

mosquito-borne virus response level, mosquito species, and meterological conditions. As 

with larval treatment thresholds, adult thresholds are subject to change to respond to 

changes in mosquito populations, disease levels, or other factors that affect public health 

(Boyce 2005).

If efforts to control immature mosquitoes fail to prevent the adult mosquito population 

from exceeding thresholds, and WNV and/or WEE or SLE are detected within or near the 

Refuge, the District proposes to treat infested areas with a mosquito adulticide. The District 

proposes to continue to use currently labeled adulticides containing active ingredients 

pyrethrin (ex. Pyrocide 7338TM, Evergreen 60-6TM), and phrethroids (ex. ScourgeTM). Though 

the District has also proposed usage of the adulticide Trumpet (Naled) if necessary, this 

particular chemical has not been used at the Refuge to date.

Pyrethrins are non-systemic contact poisons which quickly penetrate the nerve system 

of the insect and cause paralysis and subsequent death (ETN 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). Trumpet (Naled) is a non-systemic, broad-spectrum 

organophosphate insecticide which affects the nervous system of adult mosquitoes and 

other insects by cholinesterase inhibition. The products SYMVCD proposes, Pyrocide 

7338, Scourge and Trumpet, are applied as an ultra-low volume (ULV) fog by ground. To 

minimize pesticide drift, dispersing vehicles will follow routes on existing roads set up to 

fog downwind or outside buffers of 300 feet from areas supporting listed or proposed special 

status species. All chemical applications will occur when wind speeds are between 2 and 8 

mph. 

Adult mosquito control measures were applied only once in 1998 to 5 acres (0.09 gallons 

of Scourge) and once in 1999 to 4 acres (0.05 gallons of Pyrocide 7338). Both adulticide 

applications were performed at the same location, at a drain in an agricultural field, due 

to the large population. In August of 2005 the number of human WNV cases and rate 

of infected adult mosquitoes were so high that SYMVCD initiated aerial applications of 

pyrethrin over significant portions of Sacramento County. The Refuge received ultralow volume (ULV) ground applications of pyrethrin on 16 occasions between July 28 and 

October 12, 2005. As of August 18, 2006, 16 human cases of WNV have been documented in 

Sacramento and Yolo counties and the Refuge has had adulticides applied 12 times.

Availability of Resources: Monitoring and control will not require refuge personnel. 

The District is responsible for coordination of monitoring and control through the Refuge 

Manager or the Assistant Refuge Manager. In order to monitor treatment of wetland, 

moist soil and riparian areas, it is estimated that 5% of a full-time employee’s time would 

be required. Monitoring of treatments would include observations of sprayed areas before 

and after treatment and coordination of permitting, documentation and record keeping. 
150 Stone Lakes NWR Comprehensive Conservation Plan

Additional funding would be required if a detailed, long-term study were to be conducted to 

determine effects of mosquito treatment on Refuge resources. 

Anticipated Impacts of the Use: The impacts of monitoring will be confined to pathways 

and 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. Placing and checking of light or CO2 traps may also create a transient 

impact from footsteps on the vegetation going to and from the traps. 

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. The possible effects of the larvicides Bacillus spp. and 

methoprene, the pupacide Agnique, and the adulticides will be discussed separately.

Bti

Bti has practically no acute or chronic toxicity to mammals, birds, fish or vascular plants 

(USEPA 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 crustaceans (Brown et al. 

2002, Brown et al. 2000, Garcia et al. 1980, Lee and Scott 1989, 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. 
Stone Lakes NWR Comprehensive Conservation Plan 151

Bsp

Bsp has slight to practically no acute mammalian toxicity, practically no acute avian toxicity, 

slight to practically no acute fish toxicity, and slight aquatic invertebrate toxicity (USFWS 

1984, and FCCMC, 1998). Insecticidal activity may persist longer than 20 days because Bsp 

can reproduce and sporulate in larval cadavers and can retain its larvicidal properties after 

passing through the gut of a mosquito. Bsp is insoluble in water. Spores and toxin become 

suspended in the water column and retain insecticidal activity in water with high organic 

matter content and suspended solids. Because Bsp is a more recently developed larvicide 

than Bti, there are fewer studies that have examined the non-target effects of this pesticide. 

The data available, however, indicate a high degree of specificity of Bsp for mosquitoes, 

with no demonstrated toxicity to chironomid larvae at any mosquito control application rate 

(Mulla, 1984, Ali, 1986, Lacey, 1990). Therefore risks to sensitive wildlife resources resulting 

from direct exposure to a single Bsp application and indirect food chain effects are expected 

to be negligible. However, the ability for a population to re-colonize a wetland following 

multiple larvicide treatments would depend on the intensity and frequency of applications at 

different spatial scales.

Agnique (Monomolecular film)

Monomolecular film has practically no acute mammalian or avian toxicity, and slight acute 

fish toxicity (USEPA 2000, USFWS 1984). The risk quotient for mammals is well below 

the EPA endangered species level of concern (LOC) indicating negligible risk resulting 

from direct exposure, Table 1 (Urban and Cook 1986). Risk quotients for birds and fish 

exceed EPA endangered species LOCs indicating a hazard to those taxa resulting from 

direct exposure. Risk to fish will be limited by the insolubility of monomolecular film in 

water. Monomolecular film is insoluble in water, average persistence in the environment 

is 5 to 14 days (Borgerding 2001). Indirect effects to animals dependent on invertebrate 

food resources are possible resulting from a reduction of those resources caused by 

monomolecular film. The magnitude of the impact would depend on the aerial extent of the 

treatment, the number of treatments, treatment frequency and the location of the treatment 

relative to the areas used by invertebrate feeding animals. 

Table 1. Monomolecular film risk quotients.

Animal Acute tox (ppm) EEC (ppm) RQ LOC (ES)

bird > 5000 (8 D LC 50) 850 (short grass) 0.2 0.1

fish 98 (96 hr LC 50) 2600 (6" water) 26.5 0.05

mammal >20,000 (LD 50) 850 (short grass) 0.004 0.1

EEC calculated using a rate of 0.5 gal/ac (3.6 lbs ai/ac)

LD 50 for mammals converted to 1 Day LC50 using a conversion factor of 0.1 for RQ calculation 

Methoprene

Methoprene has moderate acute fish toxicity, slight acute avian toxicity, and practically 

no acute mammalian toxicity (USEPA 2000, USFWS 1984). In mallard ducks, dietary 

concentrations of 30 parts per million (ppm) caused some reproductive impairment (USEPA 

1991). This figure exceeds the estimated environmental concentration by a factor 10 (Table 

2). Methoprene residues have been observed to bioconcentrate in fish and crayfish by 

factors of 457 and 75, respectively (USEPA 1991). Up to 95 % of the residue in fish was 

excreted within 14 days (USEPA 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 (Table 1) 

(Urban et al. 1986). In field studies no detectable adverse effects to breeding red-winged 
152 Stone Lakes NWR Comprehensive Conservation Plan

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 

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 2006). Methoprene is 

highly toxic to aquatic invertebrates with a 48 hour EC50 of 0.89 ppm for Daphnia magna 

(USEPA 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, 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 (USEPA 1991). Degradation rates are roughly equal in freshwater 

and saltwater systems and are positively correlated to temperature (USEPA 1991). 

Adulticides

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. One 

organophosphate, Trumpet (Naled), is proposed for use at the Refuge but has not been 

applied to date. The two pyrethroid products proposed for use at the Refuge, Pyrocide 7336 

and Sourge, are both synthetic pyrethrins.

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). Pyrethrins are toxic to all invertebrates, but the method of application via ultra-low 

volume atomizer limits toxicity and contact with non-targets. To minimize pesticide drift, 

applications would take place during the evening hours, when wind speeds are reduced 

and temperatures decreased. The evening is also the period when mosquito activity is the 

greatest.

Naled is a fast acting, nonsystemic contact and stomach organophosphate insecticide used 

to control aphids, mites, flies and mosquitoes. Naled is highly to moderately toxic via the 

oral route. It is moderately toxic through skin exposure, may cause skin rashes and skin 

sensitization and may be corrosive to the skin and eyes. Naled is highly to moderately toxic 

to birds. The reported acute oral LD50 for naled is 52 mg/kg in mallard ducks, 65 mg/kg 

Table 2. Risk assessment for Methoprene.

Animal Acute Tox (ppm) *EEC (ppm) RQ LOC (ES)

Bird > 4640 (8 D LC 50)** 3.0 (short grass) 0.0006 0.1

Fish 0.4 (96 hr LC 50) 0.01 (6 inches) 0.025 0.05

Mammal > 34,000 (LD 50) 3.0 (short grass) 0.00001 0.1

*EEC calculated using a rate of 0.013 lbs ai/ac (1.0 fluid oz/ac Altosid 20 % methoprene)

**LD 50 for mammals converted to 1 Day LC50 using a conversion factor of 0.1 for RQ calculation
Stone Lakes NWR Comprehensive Conservation Plan 153

in sharp-tailed grouse, 36-50 mg/kg in Canadian geese, 120 mg/kg in ring-neck pheasants. 

Naled is highly to moderately toxic to fish and may be very highly toxic to aquatic 

invertebrate species (ETN 1996).

However, Trumpet (Naled) is practically nonpersistent in the environment, with reported 

field half-lives of less than 1 day. It is not strongly bound to soils and is rapidly broken down 

if wet. Soil microorganisms break down most of the naled in the soil. It therefore should not 

present a hazard to groundwater (ETN 1996).

Threatened and Endangered Species

The Refuge provides potential habitat for the following endangered species: giant garter 

snake, Sacramento splittail, Delta smelt, valley elderberry beetle, vernal pool tadpole 

shrimp and vernal pool fairy shrimp. 

Vernal Pools

The growth regulator Methoprene (Altosid or A.L.L) can have deleterious effects on 

vernal pool shrimp by delaying the development of adult shrimp and thus the number of 

eggs laid before the pools dry up (Lawrenz 1984). Because of the effects of Methoprene 

on fairy shrimp and a lack of information on how long the agent remains in the soil, use of 

the larvicide methoprene within vernal pools or swales at any time, in either wet or dry 

conditions, is prohibited (USFWS 2001). 

The majority of vernal pools and seasonal swales will be dry during the main pesticide 

application period (June-October). In general, vernal pool habitats are not significant 

mosquito-producing habitat and should not require chemical treatments for control of 

mosquito larvae because they are sufficient predators in naturally functioning vernal pools to 

keep larval numbers below the treatment threshold. In the event that the use of a larvicide 

does become necessary in the vicinity of vernal pools, Bti, which is relatively specific to 

mosquitoes and flies, will be the agent of choice. 

The majority of the vernal pools at the Refuge occur on the Wetland Preserve property 

which became part of the Refuge under a conservation easement in 2004. During the 

spring of 2004, before the conservation easement went into effect, numerous vernal pools 

were treated with Bti. Relatively warm spring temperatures in 2004 likely contributed to 

elevated larval populations, but other factors may also be involved. The mosquito abatement 

district had increased larval monitoring in the area because the Wetland Preserve property 

is adjacent to a housing development and WNV had recently arrived in Sacramento county. 

Many of the vernal pools in the Wetland Preserve property are man made mitigation pools 

that may not be functioning as a naturally occurring vernal pool would. The hydrologic 

regime and/or diversity and number of invertebrates in man made vernal pools may create 

more favorable conditions for mosquito larvae in that mitigation pools may hold water 

longer and may harbor fewer invertebrates that prey on mosquito larvae (Stan Wright pers. 

comm.). The increase in grazing that has occurred since the Service assumed management 

may reduce mosquito larvae populations by increasing water movement in the vernal 

pools due to wind action. Future mosquito abatement activities in the Wetland Preserve 

property will be closely monitored by Refuge staff to avoid conflicts between wildlife habitat 

improvement goals and mosquito control goals. 

Giant Garter Snake

Mosquito control activities in giant garter snake habitat may affect giant garter snakes by 

harassment or injury from vehicle use. The District will only operate vehicles in existing 

roads; therefore, harassment or injury from vehicle use would occur only if snakes are in 

the roadway. Regarding the effects of the proposed pesticides, a Fish and Wildlife Service 
154 Stone Lakes NWR Comprehensive Conservation Plan

sponsored study indicated that the short-term effects of adulticides approved for mosquito 

control on the Sacramento NWR Complex did not significantly reduce abundance or biomass 

of the snake’s prey items, macro-invertebrates and fish, in treated wetlands (Lawler et. 

al. 1997). However, no information is available on the toxicity of the proposed pesticides 

directly to the giant garter snake. Without further information, it must be assumed that 

exposure of giant garter snakes to these chemicals could result in direct impacts, such as 

loss or sublethal effects to individual animals. Adverse effects to the giant garter snake 

from mosquito control activities will therefore be minimized by avoiding any wetland 

habitat suitable for giant garter snakes while applying chemical treatments for control of 

mosquitoes. 

Valley Elderberry Longhorn Beetle

Adverse effects on the valley elderberry longhorn beetle are not likely since the main 

mosquito abatement period (June-September) does not coincide with the period of adult 

beetle emergence (late April through mid-May or early June). Also, the riparian corridors 

that house the valley elderberry longhorn beetle, generally do not require treatment with 

chemical control agents. If control measures are needed in these areas, some granular 

applications of Bti or Altocid (Methoprene) may be used during February or March when 

adult beetles are not present.

Delta Smelt and Sacramento Splittail

Both Delta smelt and Sacramento splittail are not likely to be adversely affected by 

mosquito abatement activities. Delta smelt and Sacramento splittail have never been 

recorded within Refuge waterways. In addition, the open water areas of the Refuge in 

which these species could occur are not considered mosquito production areas and would not 

be subject to any chemical treatment (USFWS 2001).

In general, species of concern will not be adversely affected by mosquito control activities 

provided the conservation measures detailed in the Intra-Agency Formal Section 7 

Consultation on Pest Management Activities and the stipulations contained herein are 

followed (USFWS 2001). 

Wetlands and Waterfowl

The Refuge was established to provide habitat for migratory birds, in particular waterfowl. 

The District will continue to minimize disturbance and non-target effects to wildlife by 

limiting mosquito abatement activities between October 15 and February 15 when the 

majority of migratory bird species would be arriving on the Refuge. However, since the 

District continues to treat until temperatures have dropped sufficiently to reduce the 

abundance of mosquitoes, in warmer years there may well be a longer period of overlap 

between the arrival of migrants and continued mosquito abatement activities. In addition, 

if mosquito thresholds are exceeded, or the presence of WNV is detected in or around the 

Refuge, then the District may need to extend mosquito surveillance and control into late fall.

In some years, most notably 2004, the District has applied Bti or planted mosquito fish as 

early as March when some migratory waterfowl may still be lingering before departing 

on their spring migration. However, Bti and Bsp have not been found to be toxic to birds 

(USFWS 2001). In addition, it has been found that birds are not negatively affected by 

utilizing foods exposed to Bti or methoprene (Niemi et al. 1999). Although physico-chemico 

data and environmental fate data are limiting, Bacillus spp. are virtually non-toxic to 

mammals, birds and fish. During the last 8 years methoprene has not been applied prior 

to June and was applied as late as October in only one instance. Thus, applications of 

methoprene have not directly or indirectly affected migratory birds utilizing the Refuge 

because migratory birds have not been present during mosquito abatement activities.
Stone Lakes NWR Comprehensive Conservation Plan 155

There is not likely to be much impact on geese and swans from pesticides because they 

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. In contrast, ducks are known to be opportunistic feeders on both plants and 

invertebrates, utilizing 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). Waterfowl in general tend to 

feed on seeds when they reach their wintering areas, perhaps to regain energy lost during 

long flights (Heitmeyer 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 diet shifts to invertebrates after mosquito treatments are expected to 

be reduced in frequency, thereby allowing the invertebrate populations to recover.

Resident Waterfowl

Birds utilizing the Refuge during the summer months and early fall, when most of the 

mosquito abatement occurs, could have a greater risk of being affected by pesticide 

applications. These species include herons, egrets, white pelicans, mallards and wood ducks. 

The pesticides being applied at the Refuge have not been shown to be toxic to birds, but 

could potentially affect resident waterfowl indirectly by reducing invertebrate food sources. 

Shorebirds could also be of concern, since they feed on a wide variety of invertebrates all 

year, feeding which intensifies at the onset of spring migration. However, 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 two years before treatment and three years 

after treatment of both Bti and methoprene applications and found no negative effects. 

Jensen et al (1999) found that no decreases were detected in the biomass or abundance of 

aquatic invertebrates in seasonal wetlands from ultra-low volume applications of pyrethrin, 

permethrin or malathion. 

Public Review and Comment: If through monitoring it is determined that targeted 

mosquito species; 1) are known carriers of Encephalomyelitis viruses and 2) occur in 

densities that warrant control, the public will be notified. However, given the nature of 

potentially serious health risks and the rapid development of mosquito larvae, applications 

may occur simultaneously with public notification or before public notice. 

Several written comments were received suggesting technical corrections to the CCP and 

the Integrated Pest Management (IPM) plan for mosquito associated threats. One oral 

comment suggested that vector control should be a higher priority in the CCP. 

Response: All of the technical corrections recommended were made to the CCP and 

mosquito IPM plan. Control of mosquito associated threats continues to be a high priority 

on the Refuge as evidenced by the preparaton of the IPM plan for mosquito associated 

threats and the close working relationship between the Refuge and the Sacramento Yolo 

Mosquito Vector Control District. 

Determination (Check One Below)

_______ Use is not compatible 

 X Use is compatible
156 Stone Lakes NWR Comprehensive Conservation Plan

Stipulations Necessary to Ensure Compatibility:

1. The District will notify the Refuge manager as soon as possible when mosquito 

larval thresholds are exceeded and ground treatment is warranted by calling refuge 

headquarters.

2. When adult thresholds are exceeded, and in the event of a planned adulticiding or aerial 

application of any kind, the District will contact and personally coordinate with the 

Refuge Manager or Assistant Refuge Manager prior to conducting the treatment.

3. The District will notify the Refuge Manager in the event of detection of virus activity 

within or near the Refuge and the method of disease surveillance yielding positive results.

4. The District will provide the Refuge Manager with an annual report summarizing 

mosquito control activities during the previous year.

5. The District has and will continue to consider environmental conditions, including water 

temperature, density of mosquito larvae and presence of mosquito predators, when 

deciding mosquitoes on the Refuge pose a serious threat to human health and whether to 

treat.

 6. Access will be prohibited in closed areas on Wednesdays and Sundays during the 

waterfowl hunt season.

7. Application of mosquito control measures is to be conducted in accordance with approved 

Pesticide Use Proposals.

8. Mosquito control will be authorized on an annual basis by a Special Use Permit (SUP). 

The SUP conditions will stipulate that all mosquito control work will be carried out under 

the guidance of pre-approved Pesticide Use Proposals.

Justification: 

For many years the Refuge has worked cooperatively with the District and its associated 

mosquito control activities. After a review of these activities, the Refuge has determined 

that allowing these uses to continue would not interfere or derogate from the purpose for the 

Refuge, nor the mission of the National Wildlife Refuge System.

 The Refuge is located within a 10 mile radius of various urban and rural communities. 

Species of mosquito like Culex tarsalis, Anopheles freeborni, Aedes melanimon and Aedes 

nigromaculis, are found on the Refuge and are capable of dispersing various miles to obtain 

a blood meal. With the exception of Culex tarsalis, the remaining fore mentioned species 

are capable of dispersing 5-10 miles; Culex tarsalis is known to disperse over 25 miles. 

All species are known to be vectors for Saint Louis encephalitis, California encephalitis 

and western equine encephalitis; additionally, C. tarsalis is particularly known to transmit 

West Nile virus. Mosquito control is conducted on Refuge lands to prevent populations of 

adult mosquitoes from rising to levels that could pose a public health hazard or significant 

nuisance to neighboring communities, following the guidance of the stipulations within 

this document. Cooperative efforts between the Refuge and the District have successfully 

controlled larval mosquito populations on the Refuge to the extent that adulticide 

applications have only been necessary twice over the last 8 years. Since the approved 

adulticides are generally more toxic to wildlife and wildlife food sources than larvicides, it is 

in the best interest of wildlife to minimize adulticide applications.
Stone Lakes NWR Comprehensive Conservation Plan 157

Because mosquito treatment occurs during the early weeks of fall flood-up before most 

migratory birds have arrived, and since the frequency of treatments are low and spaced 

apart on a per unit basis, overall effects to non-target organisms are not expected to 

be significant. In addition, the number of treatment days per year is fairly low, and if 

the applicator 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 re-analyzed on the basis on new evidence.

Mandatory Re-Evaluation Date (provide month and year):

Mandatory 15-year Re-Evaluation Date (for priority public uses)

February, 2017 Mandatory 10-year Re-Evaluation Date (for all uses other than priority 

public uses)

NEPA Compliance for Refuge Use Decision (check one below):

_______ 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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Stone Lakes NWR Comprehensive Conservation Plan 159

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Stone Lakes NWR Comprehensive Conservation Plan 161

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162 Stone Lakes NWR Comprehensive Conservation Plan

Compatibility Determination for Grazing Programs on the Stone Lakes National 

Wildlife Refuge

Use: 

Grazing program to provide (1) suitable habitat for wintering sandhill cranes, arctic nesting 

geese such as Aleutian cackling geese, shorebirds and breeding habitat for nesting grassland 

birds such as Western meadowlark; (2) expand native grasses (3) reduce fire danger by 

reducing thatch layer (Alternative B, Stone Lakes National Wildlife Refuge Comprehensive 

Conservation Plan Environmental Assessment).

Refuge Name:

Stone Lakes National Wildlife Refuge

 

Establishing and Acquisition Authorities:

Stone Lakes National Wildlife Refuge (NWR) was established in 1994 under the authority 

of the Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956, the 

Migratory Bird Conservation Act, and the Endangered Species Act of 1973. The approved 

refuge boundary contains about 18,000 acres, of which the Service owns or manages 

approximately 6,000 acres. Additional funding sources used to acquire land include: the 

California Environmental License Plate Fund, the Cigarette and Tobacco Product Surtax 

(California Proposition 99, 1988), the North American Wetland Conservation Act, the Land 

and Water Conservation Fund, the Sacramento County Environmental Mitigation Grant/

Packard Foundation, the Central Valley Improvement Act, the National Fish and Wildlife 

Fund, the Trust for Public Land Grant/Packard Foundation, the City of Sacramento and the 

CalFed Bay Delta Program.

Refuge Purpose(s): 

Stone Lakes NWR purposes include the following: 

“... for the conservation of the wetlands of the Nation in order to maintain the public benefits 

they provide and to help fulfill international obligations contained in various migratory bird 

treaties and conventions ...” (Emergency Wetlands Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.’ (Migratory Bird Conservation Act of 1929)

“... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...@ (Endangered Species Act of 1973) 

National Wildlife Refuge System Mission: 

 “The mission of the National Wildlife Refuge System (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” (National Wildlife 

Refuge System Administration Act of 1966, as amended [16 U.S.C. 668dd-668ee]).
Stone Lakes NWR Comprehensive Conservation Plan 163

Description of Use:

The Stone Lakes National Wildlife Refuge (Refuge) will administer a grazing program on 

the North Stone Lake (2,791 acres) and South Stone Lake (582 acres) Units of the Refuge. 

The North Stone Lake Unit is comprised of approximately 1,900 acres of mostly non-native 

grassland and 891 acres of open water, riparian and wetland habitat. The Gallagher tract of 

the South Stone Lake Unit is comprised of approximately 45 acres of irrigated pasture. The 

Sun River tract of the South Stone Lake Unit consists of 140 acres of irrigated pasture, and 

397 acres of seasonal, permanent wetlands, open water and riparian habitats. 

Grazing has been occurring on the properties for over 50 years. The Refuge will continue 

to administer this use as outlined in this Compatibility Determination. Although grazing 

is not identified as a wildlife dependent public use by the National Wildlife Refuge System 

Improvement Act of 1997, grazing will allow the Refuge to manage mostly non-native 

grassland habitats on the Refuge for the benefit of wildlife and native plants while reducing 

the fire danger to adjacent communities. This use will provide short grass foraging and 

loafing habitat to a variety of wintering migratory birds such as the greater sandhill crane 

(Grus canadensis tabida), arctic nesting geese including Aleutian cackling goose (Branta 

hutchinsii leucopareia) and white fronted goose (Anser albifrons), shorebirds including 

white faced ibis (Plegadis chihi), long billed curlew (Numenius americanus) and black 

bellied plover (Pluvialis squatarola). These grasslands also provide nesting and foraging 

habitat for western meadowlark (Sturnella neglecta), horned lark (Eremophila alpestris), 

northern harrier (Circus cyaneus), white tailed kite (Elanus leucurus) and Swainson’s 

hawk (Buteo swainsoni), and have the potential to provide habitat for nesting and wintering 

burrowing owls (Athene cunicularia), Savannah sparrows (Passerculus sandwichensis) and 

grasshopper sparrows (Ammodramus savannarum). Habitat consists of introduced (> 70% 

annual rye [Lolium multiflorum]) and native grasses (including creeping wildrye [Leymus 

triticoides], saltgrass [Distichlis spp.] and meadow barley [Hordeum branchyntherum])as 

well as other forbs and associated native plant food resources. 

Only the grazing of cattle is to be considered on the Refuge; grazing by sheep (Ovis aries), 

goats (Capra hircus), or other creatures such as bison (Bison bison) will not be considered. 

During drought years or years of low rainfall, cattle will not be allowed to graze on the 

Refuge. 

The timing of the placing of cattle on the Refuge are termed “turn in dates” (November 

1 or slightly later) and are adjusted year to year based upon the date of the first effective 

germinating rainfall, and the amount of dry forage available in the fall (Stechman 1995). The 

timing of removing cattle from the Refuge is termed “turn out dates” and is determined 

solely on the amount of residual dry matter (RDM) within the unit, but will be no later than 

July 15th. If and when 800 lbs per acre, of RDM, or less is achieved cattle will be removed 

from the unit. 

The unit of measure used to summarize the quantity of cattle grazing on the Refuge is 

termed Animal Unit Month (AUM). AUM is defined as the amount of forage needed by an 

“animal unit” (AU) grazing for one month (USDA-NRCS 2004). An AU is defined as one 

mature 1,000 pound cow and her sucking calf. An assumption in this definition is that a cow 

nursing her calf will consume about 26 pounds of dry matter per day. Other types of livestock 

are assigned AUM equivalents based on body size and consumption of dry matter.

The optimal time for grazing in the Central Valley begins in November and may continue 

through mid July depending on winter and spring rainfall. Prior to the beginning of the 

grazing season, an assessment is made to determine the amount of residual dry matter 

(RDM) available to the cattle. The number of cattle allowed to graze on the Refuge, for a 
164 Stone Lakes NWR Comprehensive Conservation Plan

specific amount of time, varies with the amount of local rainfall. Because grazing on the 

Refuge supports various wildlife populations, this RDM level is linked to the needs of wildlife 

and not the needs of the cattle. The RDM is determined by clipping, drying, and then 

weighing the amount of RDM in representative samples from the unit cattle are to graze and 

varies upon temperature, monthly rainfall and the density of new grass/forb growth. 

The Refuge has developed a 5-year grazing management plan with the assistance of 

the Natural Resource Conservation Service that promotes variability in grass height 

and density among the five dry pasture units to provide habitat for a suite of grassland 

dependent species. This plan rotates grazing pressure (low, medium and high) in five 

pastures (see Figure 1) resulting in a range of grass heights and densities (see Table 1). 

The rotational grazing should result in higher quality habitat for species that inhabit short 

grasses such as burrowing owls, without impacting other grassland dependent species. 

A monitoring program will be implemented to determine if increasing grazing rates and 

rotating grazing pressure through the units will have the desired effects of providing a 

variety of nesting, foraging and breeding cover for a variety of birds and other wildlife. If 

the RDM level drops below 800 lbs/acre, prior to or anytime during the grazing season, the 

Refuge manager may request that the grazing permit holder reduce the number of cattle 

grazing in that unit or remove them all together in order to prevent degradation of the 

resources in the unit. 

Table 1. Residual Dry Matter (RDM) targets over a five year period on the North Stone 

Lake Unit of the Stone Lakes National Wildlife Refuge in California.

RDM Value at the End of the Grazing Season (Nov – June)*

Pasture Year 1 Year 2 Year 3 Year 4 Year 5

A Medium Low Medium High Low

B High Medium Low Medium Medium

C Low Medium High Low Medium

D Medium High Low Medium High

E Low Low Medium Low Low

F** Medium Medium Medium Medium Medium

*RDM values – Low(1200-1750 lbs/acre), Medium (1750-2500 lbs/acre), High (+2500 lbs/acre).

** Southwestern portion of South Irrigated Pasture (Fig. 1). Cattle will be in unit for 30-60 days 

from March-May to control weeds.

Grazing in the irrigated/wet meadow units (371 acres) on the North Stone Lake and South 

Stone Lake units begins in mid summer, corresponding to the removal of cattle from the 

dry pasture and continues until approximately November 1. Grazing rates typically range 

between 1.1 – 1.3 acres per AUM. These pastures, which are not grazed during the winter 

season, are heavily used by cranes, geese and shorebirds.

The grazing cooperator is chosen following guidance in U.S. Fish and Wildlife Service 

Refuge Manual under heading 5 RM 17. At the time of this writing, there are no anticipated 

changes to grazing on the Refuge. 
Figure 1. Map of the North Stone Lake Unit of the Stone Lakes National Wildlife Refuge showing the 

designation of pasture units and location of perimeter and cross fences in blue.
166 Stone Lakes NWR Comprehensive Conservation Plan

Availability of Resources:

The assistant refuge manager, under the direction of the project leader, will manage 

the grazing program. The permittee, working under a Cooperative Land Management 

Agreement, will accomplish certain facility management and improvement projects under 

the direction of the assistant manager. Accomplishments will be in direct support of 

the Refuge grazing program; these projects may include maintenance or improvements 

of existing facilities or installation of new facilities. Projects may include: deep well 

construction and maintenance; installing and/or maintaining water control structures, 

watering troughs; fence installation, repair, and/or removal; sign repair, removal, or 

installation; gate installation; noxious weed control; road building and maintenance; parking 

lot maintenance; and vegetation control around facilities. Facilities that are installed 

primarily for Refuge purposes are constructed or maintained at Refuge expense. All 

projects will be agreed upon before the beginning of the grazing season and will directly 

support the unit being grazed.

Rates charged per AUM are based on a survey of grazing rates in the area and were done 

on an upward sliding scale. Rates are now fixed until the end of the current grazing contract 

with the County of Sacramento which ends in 2008. Rates will then be renegotiated based 

on a survey of grazing rates in the area. 

At the end of each grazing season, the permittee submits information that includes AUMs 

per month per grazing unit and the cost of various projects completed on the unit that year. 

The project list is then revised for the following year. Work contributions of this type will be 

associated with improvement projects for the particular grazed unit. 

The Refuge receives adequate funding to cover the costs associated with management of 

the grazing program including the RDM assessment conducted at the end of every grazing 

season. Staff costs associated with this use emanates from the annual review of Special Use 

Permits, Cooperative Land Management Agreement and monitoring the impacts of this 

use as outlined in the grassland management plan. Annual costs to manage the grazing 

programs averages $25,000, which includes all costs associated with monitoring, weed 

control, law enforcement, improvements and planning activities. 

Anticipated Impacts of the Use: 

To provide this use, the Refuge has adequate staff which includes biological, administrative 

and managerial personnel. The grazing program results in both long and short term effects, 

both negative and positive. The following is a list of possible short and long-term negative 

impacts to wildlife resources from grazing: trampling of desirable vegetation, disturbances 

to ground nesting species, trampling of rodent burrows, soil compaction especially during 

wet periods and erosion of the bank along North Stone Lake. The following activities can 

minimize these negative impacts associated with grazing: fencing off sensitive habitats, 

development of alternative watering sources for cattle to drink from, allowing the use in 

years of adequate rainfall only and supporting grazing within the same unit areas and not 

moving animals to un-grazed or sensitive areas. 

Conversely, short and long-term positive impacts of the grazing program include: an overall 

reduction of undesirable, non-native vegetation; re-establishment of native grass, forb, and 

shrub communities; reduced fire danger to surrounding communities; and increased habitat 

for grassland dependent species. Prior to reestablishment of a grazing program by the 

Refuge, the North Stone Lake Unit was left idle for approximately 12 years. Over that time, 

the grass became dense with vegetation reaching 6-8 feet tall. Bird surveys revealed no use 

by sandhill cranes, arctic nesting geese or shorebirds, although these birds used the area 

historically. Once the grazing plan was implemented, these birds returned within two years, 
Stone Lakes NWR Comprehensive Conservation Plan 167

and the, California State Endangered Species Act, listed greater sandhill crane now number 

over 300 birds. Native grass stands have also benefited from the grazing program and are 

expanding (Huitt 2003). Adjacent landowners are also satisfied with the decrease in thatch 

and the fire break that further reduces the threat of fire spreading across the property and 

onto neighboring lands.

The impact of cattle to existing water supplies is negligible and being diminished as 

alternative watering sources are being developed. Alternative watering sources help keep 

cattle from watering in the lake where they can erode the bank in high use areas. A solar 

powered well now brings water to cattle in Pastures A and B, and a pipeline from the well at 

the HQ will bring water to cattle in Pasture E. A well already exists in Pasture D and plans 

are being finalized to construct an additional well in pasture C.

Much of the topography is flat with little sedimentation and erosion entering the two arms 

of North Stone Lake. The south arm of the lake which is surrounded by riparian vegetation 

has been fenced off to cattle, as have the other sensitive riparian zones on the property. 

Bird surveys indicate the grazing program provides a significant benefit to various species 

of concern that winter in the Central Valley including the greater sandhill crane, white faced 

ibis, long billed curlew, Aleutian cackling goose and white fronted goose. Furthermore 

initial studies of nesting songbirds found that western meadowlarks nested in a wide range 

of grass heights below 3.5 feet, but were not found in areas where the grass exceeded this 

height. 

Cowbirds (Molothrus ater) are found over the entire Refuge and parasitize nests of various 

species in riparian areas. Therefore 85% of existing riparian areas have been fenced off 

to decrease suitable habitat for cowbirds. Whether the grazing program will contribute 

to increases in the cowbird population by providing additional foraging areas is unknown. 

Large mixed flocks of blackbirds are seen in the spring and fall, but no cowbirds were 

recorded during point count surveys done the spring of 2006. Efforts to fence off riparian 

remaining riparian areas will continue. 

Impacts to known cultural resources from this use are negligible. Tremaine and Associates 

(2006) completed a survey of the entire property in 2005, and all cultural resource sites that 

could be impacted by cattle were fenced off. Furthermore, the grazed units are closed to the 

public, further protecting these sites. Any ground-disturbing activities will be coordinated 

with the Service’s Regional Archaeologist, in order to preserve the Refuge’s archaeological 

and historic resources.

The Draft Comprehensive Conservation Plan (USFWS 2006) identifies the need to develop 

additional information relating to the effects of grazing on resident and migratory species. 

While the effects have been determined to be generally positive, additional research and 

evaluation will allow the Refuge to refine its management strategies and objectives for 

grassland management.

Public Review and Comment: One comment recommended that the CCP should indicate 

how NEPA requirements were met for a prior cooperative agreement related to grazing. 

Another comment suggested that horses would have less impact on Refuge lands and waters 

than long-term cattle grazing. Another comment observed that the fact that grazing is an 

approved refuge use demonstrates that not all Refuge uses have to be wildlife dependent 

uses.

Response: The environmental assessment, Appendix B of the draft CCP, applies only 
168 Stone Lakes NWR Comprehensive Conservation Plan

to the current proposed action described in the draft CCP. Refuge land conservation 

efforts such as cooperative agreements are provided for under the 1992 Final 

EIS establishing the approved Refuge boundary (USFWS 1992). As stated in the 

justification below, the goals for grazing on the Refuge are to conserve, enhance, 

restore and manage Central Valley wetland, riparian, grassland and other native 

habitats to benefit their associated fish, wildlife, plants and special status species. 

Determination: (Check One Below)

 Use is not compatible

 X Use is compatible, with Stipulations

Stipulations Necessary to Ensure Compatibility:

The Cooperator is operating under the terms and conditions of a Cooperative Land 

Management Agreement (2001), special use permit and a Refuge Grazing Plan. These 

documents provide the necessary information and assistance from the Refuge to determine 

start and end dates for cattle placement and removal. 

Additional Stipulations are as follows:

• It is the responsibility of the Refuge Manager to determine fair market value of grazing, 

to issue special use permits, monitor permittee compliance and maintain up-to-date files on 

all grazing activities. 

• All cattle grazing on the Refuge would be removed no later than July 15th. 

Monitoring: 

A monitoring program will be established to provide data on residual dry matter, cover 

density, bird use, and noxious weeds. These data will establish guidelines for making 

management decisions concerning the grazing program. Maps of RDM will be compiled 

using the comparative yield method (Dudley, pers. comm.) in September or October of 

each year. The comparative yield method measures the residual dry matter by clipping 

the grass in a 1 meter square and then weighing the dried sample. This is repeated until 

the observer can determine the residual dry matter by observation rather than clipping 

grass samples. Samples are still collected to ensure accuracy of the observations. Maps are 

then compiled from the data and visual observations. Data on grass height and density is 

collected during the nesting season (March-April) using the Robel Pole Method (Harmoney 

et al. 1997). These data will be used to guide grazing rates the following year. Photo plots 

for each grazing unit will also be established and photos will be taken each year at the end 

of the grazing season (July – August). Wildlife surveys will include bimonthly waterfowl 

and shorebird surveys (November – March), greater sandhill crane surveys (September 

– March), and rookery surveys (March – June). Noxious weed surveys will include mapping 

noxious weed infestations using a hand-help GPS unit and developing and implementing 

integrated pest management techniques to control and/or eliminate target species. 

Justification:

The primary management goals guiding the grazing of the Refuge are to conserve, enhance, 

restore, and manage Central Valley wetland, riparian, grassland, and other native habitats 

to benefit their associated fish, wildlife, plants and special status species, and to conserve, 

enhance, and restore high quality migrating, wintering, and breeding habitat for migratory 

birds within the Sacramento-San Joaquin Delta of the Central Valley. The mission of 

the National Wildlife Refuge System also includes the conservation, management and 

restoration of wildlife resources. When evaluating the appropriate management direction 

for refuges, Refuge Managers are required to use sound professional judgment to determine 
Stone Lakes NWR Comprehensive Conservation Plan 169

their refuge’s contribution to biological integrity, diversity and environmental health at 

multiple landscape scales as called for in (601 FW 3[3.7B]). The grazing program is designed 

to enhance habitat for a variety of special status species including greater sandhill crane, 

Swainson’s hawk and Aleutian cackling geese. The regulated use of grazing to benefit these 

and other species clearly supports both the System mission and the purpose for which the 

Refuge was established.

With the dramatic changes to the plant communities in California over the past 150 years, 

has come an increase in the density of ground cover due to the introduction of nonnative 

grasses and forbs (Kuchler 1988). A limited grazing season can benefit the recovery 

of native perennials by reducing annual plant biomass, increasing seed production and 

stimulating native perennial production (Huitt 2003). 

Prior to the management of the property by the Refuge, the uplands were altered from their 

original native condition by the introduction of non-native grasses and intensive grazing 

practices. In order to maintain the biological integrity and diversity of the Refuge, species 

of special concern must be provided for. The use of moderate grazing to reduce the build-up 

of annual introduced grassland biomass is viewed as beneficial to species such as greater 

sandhill crane, Aleutian cackling geese and others. By restricting the intensity and duration 

of grazing, and by adhering to the stipulations for this use, the environmental health of the 

Refuge will be maintained. 

Mandatory Re-evaluation Date (provide month and year):

 Mandatory 15 year Re-evaluation Date (for priority uses)

February, 2017 Mandatory 10 year Re-evaluation (for all uses other than priority public 

uses)

NEPA Compliance for Refuge Use Decision (check one below):

 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

Dudley, Dennis. 2004. Personal Communication. Natural Resource Conservation Service, 

Madera, California.

Harmoney, K.R., K.J. Moore, J.R. George, E.C. Brummer, and J.R. Russell. 1997. 

Determination of Pasture Biomass Using Four Indirect Methods. Agronomy Journal. 

89: 665-672.

Huitt, C.C. 2003. Effects Of Grazing And Burning On Three Perennial Grassland Species 

In The Central Valley Of California: Hordeum Brachyantherum Californicum, 

Leymus Triticoides, And Carex Praegracilis. Masters Thesis, Univ. California, Davis. 

65 pp.
170 Stone Lakes NWR Comprehensive Conservation Plan

Kuchler, A.W. 1988. The Map of the Natural Vegetation of California. 909-938 pp. In: M.G. 

Barbour and J. Major (editors); Terrestrial Vegetation of California. Calif. Native 

Plant Society Special publication No. 9. 

Tremaine and Associates. 2006. Draft Pedestrian and Geophysical Archaeological Surveys of 

North Stone Lakes: Stone Lakes National Wildlife Refuge. Tremaine and Associates. 

30 pp.

Stechman, J. 1995. Grazing assessment and management recommendations, Fort Hunter 

Liggett, California. Consult. Rpt. for U.S. Army and the Nature Conservancy, Seattle, 

WA. 178p. Dec.

U.S. Department of Agriculture, Natural Resource Conservation Service (USDA-NRCS). 

2004. Technical Note No. 31. Montana Grazing Animal Unit Month (AUM) Estimator. 

Bozeman, MT. 

http://www.mt.nrcs.usda.gov/technical/ecs/range/technotes/rangetechnoteMT32.html

Viewed on July 5, 2006.

USFWS. 2004. Stone Lakes National Wildlife Refuge Draft Comprehensive Conservation 

Plan and Environmental Assessment. CA/NV Refuge Planning Office, Sacramento, 

California.
Stone Lakes NWR Comprehensive Conservation Plan 171

Appendix B. FONSI and Environmental Assessment
172 Stone Lakes NWR Comprehensive Conservation Plan
Stone Lakes NWR Comprehensive Conservation Plan 173
174 Stone Lakes NWR Comprehensive Conservation Plan
Stone Lakes NWR Comprehensive Conservation Plan 175
176 Stone Lakes NWR Comprehensive Conservation Plan

This page is intentionally left blank
Stone Lakes NWR Comprehensive Conservation Plan 177

Stone Lakes 

National Wildlife Refuge 

Comprehensive Conservation Plan Environmental Assessment

U. S. Fish and Wildlife Service

California/Nevada Refuge Planning Office

2800 Cottage Way, Room W-1832

Sacramento, CA 95825

December 2006
178 Stone Lakes NWR Comprehensive Conservation Plan

Contents

Chapter 1. Purpose of and Need for Action ............................................180

Introduction ....................................................................................................................................180

Proposed Action..............................................................................................................................180

Purpose of and Need for the Proposed Action...........................................................................180

Project Area....................................................................................................................................180

Decisions to be Made .....................................................................................................................180

Issue Identification.........................................................................................................................180

Public Involvement ........................................................................................................................180

U.S. Fish and Wildlife Service and the National Wildlife Refuge System.............................180

Refuge Purposes .....................................................................................................................180

Refuge Goals............................................................................................................................180

Chapter 2. Alternatives, Including the Proposed Action......................185

Introduction ....................................................................................................................................185

Current Management....................................................................................................................185

Features Common to All Alternatives.........................................................................................186

Mosquito Control ....................................................................................................................186

Weed Control ...........................................................................................................................186

Riparian Habitat Maintenance/Restoration on North Stone Lake Unit.........................186

Vernal Pool Management.......................................................................................................196

Hunting.....................................................................................................................................196

Boating .....................................................................................................................................196

Cultural Resources .................................................................................................................196

Alternatives Removed From Further Consideration ................................................................196

Auto Tour Route on North Stone Lake Unit and Associated Trails ................................196

Equestrian Use .......................................................................................................................197

Upland Game and Deer Hunting..........................................................................................197

Fishing Derbies.......................................................................................................................197

Alternative A: No Action...............................................................................................................197

Habitat Restoration................................................................................................................197

Migratory Birds ......................................................................................................................197

Monitoring................................................................................................................................198

Special Status Species ............................................................................................................198

Wetland, Grassland, Riparian Habitats ...............................................................................198

New Lands...............................................................................................................................198

Visitor Services........................................................................................................................198

Alternative B...................................................................................................................................199

Habitat Restoration................................................................................................................199

Migratory Birds ......................................................................................................................199

Monitoring................................................................................................................................199

Special Status Species ............................................................................................................200

Wetland, Grassland, and Riparian Habitats........................................................................200

New Lands...............................................................................................................................200

Visitor Services........................................................................................................................200

Alternative C...................................................................................................................................201

Habitat Restoration................................................................................................................201

Migratory Birds ......................................................................................................................201

Monitoring................................................................................................................................202

Special Status Species ............................................................................................................202

Wetland, Grassland, Riparian Habitats ...............................................................................202
Stone Lakes NWR Comprehensive Conservation Plan 179

New Lands...............................................................................................................................202

Visitor Services........................................................................................................................202

Proposed Action Criteria...............................................................................................................203

Chapter 3. Affected Environment..............................................................204

Chapter 4. Environmental Consequences ...............................................205

Overview of NEPA Analysis Parameters....................................................................................205

Soils ..................................................................................................................................................205

Water Quantity and Quality ..........................................................................................................206

Air Quality.......................................................................................................................................206

Plant Communities.........................................................................................................................207

Wildlife.............................................................................................................................................208

Special Status Species ...................................................................................................................210

Diseases and Toxins .......................................................................................................................211

Cultural Resources.........................................................................................................................212

Visitor Services...............................................................................................................................213

Socioeconomics ...............................................................................................................................214

Figures

Figure 1. Watershed and Ecosystem Setting............................................................................181

Figure 2. Land Status...................................................................................................................182

Figure 3. Habitat Management Alternatives ............................................................................194

Figure 4. Visitor Use Alternatives..............................................................................................195

Figure 5. Current and Projected Visitation (15 Years) ............................................................214

Figure 6. National Outdoor Recreation Totals for 2006...........................................................215

Tables

Table 1. Summary of Alternatives...............................................................................................187

Table 2. Estimated Visitor Services on the Refuge Under Alternatives A, B, and C..........216

Appendix 1: References .............................................................................218

Personal Communications.............................................................................................................220
180 Stone Lakes NWR Comprehensive Conservation Plan

Chapter 1. Purpose of and Need for Action

Introduction

This draft environmental assessment (EA) evaluates the environmental effects of three 

alternatives for managing the Stone Lakes National Wildlife Refuge (Refuge). The U.S. 

Fish and Wildlife Service (Service) will use this EA to solicit public involvement in the 

Refuge planning process and to determine whether implementation of the Comprehensive 

Conservation Plan (CCP) will have a significant effect on the quality of the human 

environment. This EA is part of the Service’s decision-making process in accordance with 

the National Environmental Policy Act (NEPA).

Proposed Action

The Service proposes to implement Alternative B, as described in this EA. More 

information is provided about Alternative B in the CCP. 

Purpose of and Need for the Proposed Action

The Refuge needs this CCP to guide Refuge management. In addition, the National Wildlife 

Refuge System Improvement Act of 1997 requires that within 15 years of its enactment, a 

CCP must be in place for all refuges established prior to 1997.

Project Area

The Refuge was established in 1994, becoming the 505th refuge in the National Wildlife 

Refuge System. The Refuge boundary encompasses about 17,640 acres, including a core 

Refuge of about 9,000 acres, and a 9,000-acre “Cooperative Wildlife Management Area” 

(USFWS 1992). The Service actively manages about 6,000 acres. The Refuge is located in 

the Sacramento/San Joaquin River Delta (Figure 1). It is in the Beach-Stone Lakes Basin, 

found within the Sacramento Valley in the southwestern part of Sacramento County. It lies 

about ten miles south of the city of Sacramento, straddling Interstate Five from the town 

of Freeport south to Lost Slough (Figure 2). The Refuge provides wintering habitat for 

migratory waterfowl and other waterbirds in the Pacific Flyway (Figure 1). It is surrounded 

by privately owned nonnative grassland used for pasture, agricultural croplands and dense 

urban development.

Decisions to be Made

Based on the analysis documented in this draft EA, the California/Nevada Operations 

Manager must determine the type and extent of management and visitor access that 

will occur on the Refuge and whether the selected management alternative would have a 

significant effect on the quality of the environment.

Issue Identification

The Service identified issues, concerns and opportunities through early planning discussions 

and the public scoping process. This process began with the mailing of the first planning 

update in July 2002. The public also provided comments in writing and through personal 

communications. For a discussion of the planning process and issues raised, please see 

Chapter 2 of the CCP. 

The planning team helped to further define the issues. The planning team includes 

Service employees from the Stone Lakes National Wildlife Refuge Complex office and the 

California/Nevada Refuge Planning Office.
Stone Lakes NWR Comprehensive Conservation Plan 181

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182 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 183

Public Involvement

The planning team distributed three planning updates to a mailing list of about 210 

individuals, groups and agencies in July 2002, September 2002 and December 2002. The 

team held four public workshops during August and September 2002, one each in; Elk 

Grove, Sacramento, Walnut Grove and Davis, California. 

The planning staff has incorporated public input received in response to these updates and 

workshops into the CCP and EA; a summary of these comments is included in Chapter 2 of 

the CCP. The original comments are available for review in planning administrative files at 

the California/Nevada Refuge Planning Office in Sacramento, California. 

U.S. Fish and Wildlife Service and the National Wildlife Refuge System

The mission of the Service is to conserve, protect, and enhance the nation’s fish and wildlife 

and their habitats for the continuing benefit of the American people. The Service is the 

primary Federal agency responsible for migratory birds, endangered plants and animals, 

certain marine mammals and interjurisdictional fish. The responsibility to conserve our 

nation’s fish and wildlife resources is shared with other Federal agencies, State and Tribal 

governments.

As part of this responsibility, the Service manages the National Wildlife Refuge System 

(Refuge System). The Refuge System is the only nationwide system of Federal lands 

managed and protected specifically for wildlife and their habitats. The mission of the 

Refuge 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 Refuge is managed as part of the Refuge System in accordance with the National 

Wildlife Refuge System Administration Act of 1966 as amended by the National Wildlife 

Refuge System Improvement Act of 1997, and other relevant legislation, Executive Orders, 

regulations, and policies. Chapter 1 of the CCP summarizes these major laws, regulations, 

and policies and describes the goals of the Refuge System.

Refuge Purposes

The Emergency Wetlands Resources Act of 1986, the Fish and Wildlife Act of 1956 and the 

Migratory Bird Conservation Act are the establishing authorities for the Refuge.

The primary Refuge purposes are:

 “... for the conservation of the wetlands of the Nation in order to maintain the public 

benefits they provide and to help fulfill international obligations contained in various 

migratory bird treaties and conventions ...” 16 U.S.C. §§ 3901(b) (Emergency Wetlands 

Resources Act of 1986)

“... for the development, advancement, management, conservation, and protection of fish and 

wildlife resources ...” 16 U.S.C. §§ 742f(a)(4) (Fish and Wildlife Act of 1956)

“... 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 of servitude ...” 16 U.S.C. §§ 742f(b)(1) (Fish and Wildlife Act of 1956)

“... for use as an inviolate sanctuary, or for any other management purpose, for migratory 

birds.” 16 U.S.C. §§ 715d (Migratory Bird Conservation Act)
184 Stone Lakes NWR Comprehensive Conservation Plan

“... to conserve (A) fish or wildlife which are listed as endangered species or threatened 

species .... or (B) plants ...” 16 U.S.C. §§ 1534 (Endangered Species Act of 1973) 

Further refinements in the Refuge purposes can be found in the funding sources used to 

acquire land. Grants have been provided by: City of Sacramento, County of Sacramento, 

California Wildlife Conservation Board, California Environmental Enhancement Mitigation 

Fund, California Environmental License Plate Fund, Cigarette and Tobacco Product 

Surtax, Department of Transportation-TEA 21 Fund, CALFED Bay Delta Program, North 

American Wetlands Conservation Act, Land and Water Conservation Fund, Central Valley 

Project Improvement Act, National Fish and Wildlife Foundation, David and Lucille Packard 

Foundation, The Trust for Public Land and other private donations.

Refuge Goals

Goal 1. Conserve, enhance, restore, and manage Central Valley wetland, riparian, grassland 

and other native habitats to benefit their associated fish, wildlife, plants and special status 

species. 

Goal 2. Conserve, enhance and restore high quality migrating, wintering and breeding 

habitat for migratory birds within the Sacramento San Joaquin Delta of the Central Valley.

Goal 3. Provide visitors with wildlife-dependent recreation, interpretation and education 

opportunities that foster an understanding of the Refuge’s unique wildlife and plant 

communities in an urban setting. 

Goal 4. In cooperation with tribal representatives, identify and protect cultural resources on 

the Refuge and educate the public regarding Native American people and the history of the 

region. 
Stone Lakes NWR Comprehensive Conservation Plan 185

Chapter 2. Alternatives, Including the Proposed Action

Introduction

This chapter describes three alternatives for managing the Refuge: Alternative A (No 

Action), Alternative B and Alternative C. These alternatives are described below. Figures 

3 and 4 show a graphical representation of Refuge areas described in the alternatives. The 

Service’s proposed action is Alternative B. Two of the three alternatives presented in this 

chapter are “action alternatives” that would involve a change in the current management 

of the Refuge. Under Alternative A, the No Action alternative, the Service would continue 

managing the Refuge as it currently does. 

Current Management

The primary management focus of the Refuge is providing habitat for migrating, wintering 

and nesting migratory and resident birds with an emphasis on waterbirds, and a variety of 

special status species by restoring and maintaining wetland, riparian woodland, grassland 

habitats and valuable agricultural lands. 

Restoration and management of seasonal and permanent wetland habitats has been a major 

emphasis since the inception of the Refuge due to loss or conversion of this habitat in the 

Central Valley. The Refuge promotes water management regimes on managed wetland 

impoundments involving specific water draw down dates, spring irrigations and fall flood-up 

periods to produce quality habitat, primarily for wintering waterbirds. Seasonal wetlands 

are irrigated in summer to stimulate the growth of high quality waterfowl foods. Wetland 

vegetation is also manipulated periodically to maintain desired habitat conditions for 

feeding, loafing and breeding waterfowl, waterbirds and other birds. These manipulations 

can include mowing, prescribed burning, discing and noxious weed control. The Refuge 

works cooperatively with local and State agencies and private landowners throughout open 

water aquatic habitat in the Stone Lakes Basin to control mosquitoes and water hyacinth 

(Eichhornia crassipes), a non-native invasive aquatic plant.

Riparian restoration has included planting riparian trees, such as Fremont cottonwood 

(Populus fremontii), willow species (Salix sp.), box elder maple (Acer negundo var. 

californicum), valley oak (Quercus lobata) and associated understory shrubs and grasses 

and irrigating restoration areas on the Beach, North Stone, and South Stone Lake, and 

Headquarters units for three to five years to establish the plants. 

Large scale grassland management such as on the North Stone Lake Unit, includes 

promoting remnant native grasslands through use of cattle grazing, small scale prescribed 

burns, and invasive weed control. Increased use by sandhill cranes (Grus canadensis), long 

billed curlews (Numenius americanus), white fronted geese (Anser albifrons), burrowing 

owls (Athene cunicularia), and other raptors has been recorded on the unit since the grazing 

program was implemented in 1999. 

The Refuge cooperative farming program on the Headquarters Unit benefits a variety of 

migratory birds, including waterfowl, shorebirds, and sandhill cranes, that depend on small 

grains, alfalfa, tomatoes and invertebrates for a significant portion of their diet. The farming 

program maintains approximately 80 acres in corn, wheat, or grass to provide wildlife 

habitat and reduce weeds until the Service can implement expanded restoration plans. 

Service staff, cooperators, and volunteers periodically conduct biological surveys and 

monitoring within a variety of Refuge habitat, including surveys of: (1) colonial nesting 

waterbirds; (2) mistnetting of landbirds (in cooperation with the Sacramento-Yolo Mosquito 

and Vector Control District); (3) nesting success and survival of song sparrows; (4) wintering 
186 Stone Lakes NWR Comprehensive Conservation Plan

(October-May) waterfowl populations; (5) invasive weed mapping; and (6) range monitoring 

through surveys of residual dry matter.

For a complete description of the current management practices, please see “Current 

Management” in Chapter 3 of the CCP. Table 1 summarizes the alternatives analyzed in this 

environmental assessment. 

Features Common to All Alternatives

All of the alternatives contain some common features. These common features are 

presented in the following pages to reduce the length and redundancy of the individual 

alternative descriptions.

Mosquito Control

In 1993, the Service and Sacramento-Yolo Mosquito and Vector Control District (SYMVCD) 

signed a Memorandum of Understanding (MOU). According to the MOU, both parties 

agreed to cooperate to limit production and harboring of mosquitoes on Refuge habitats. 

The Service, in cooperation with SYMVCD, manages wetlands and other habitats on the 

Refuge to discourage mosquitoes by: adopting wetland design features, managing water 

regimes, planting mosquitofish (Gambusia affinis), and applying larvicides or adulticides, 

as needed. In addition, the Service and SYMVCD collaborate on other mutually beneficial 

projects, such as landbird monitoring and water hyacinth control. The Service will continue 

to participate in ongoing studies of Refuge landbirds, related to mosquito borne viruses, 

in cooperation with SYMVCD. When considering the burgeoning population immediately 

down wind of the Refuge and the recent establishment of West Nile Virus in the Central 

Valley, it is essential that the Refuge and SYMVCD continue to build on their successful 

partnership 

Weed Control

Since 1995, the Refuge has adopted an active aquatic and terrestrial weed management 

program in the Beach-Stone Lakes Basin, particularly as a founding member of the Stone 

Lakes Water Hyacinth Control Group and the Sacramento Weed Management Area. The 

Refuge and the Sacramento Regional County Sanitation District conduct treatments for 

control of water hyacinth (Eichhornia crassipes) under a Statewide National Pollution 

Discharge Elimination System (NPDES) General Permit (No. CAG990005) for discharge 

of aquatic pesticides. The Refuge and SRCSD utilize Reward (Diquat) and Aquamaster 

(glyphosphate) to control water hyacinth in the basin. Another aquatic species, Brazilian 

elodea (Egeria densa), is also abundant in waterways and may emerge as a management 

concern as opportunities for recreational boating are developed on the Refuge. 

The Integrated Pest Management methods that the Refuge uses to control weeds 

include burning, mowing, discing and herbicide application. The Refuge uses Transline® 

(clopyralid), Telar® (chlorsulfuron), Roundup (glyphosphate), and 2, 4-D, to control the 

upland weeds such as yellow starthistle (Centaurea solstitialis) and perennial pepperweed 

(Lepidium latifolium). To date, the Refuge has found chemical control to be the most 

effective method of managing water hyacinth and perennial pepperweed. Stone Lakes NWR 

is a member of the Sacramento County Weed Abatement Team.

Riparian Habitat Maintenance/Restoration on North Stone Lake Unit

Ongoing and planned improvements to the grazing program on the North Stone Lake Unit 

will continue under all alternatives and include developing alternative watering sources for 

the cattle in each pasture, bank stabilization along the SP Cut in the north irrigated pasture, 

invasive weed control, and continued monitoring of migratory bird responses.
Stone Lakes NWR Comprehensive Conservation Plan 187

Alternative A Alternative B Alternative C

No Action/Current Management

Wetland, Riparian and 

Grassland Restoration with 

Facilitated Public Use

Restore to Natural 

Conditions with SelfDirected Public Use

Habitat

Management

Riparian restoration 

and management

• 0 acres or riparian habitat 

restored

• Same as Alternative A but: • Same as Alternative A but:

• Maintain 360 acres of riparian and 

oak woodland habitat

• Maintain 425 acres of 

riparian and oak woodland 

habitat

• Maintain 385 acres of 

riparian and oak woodland 

habitat

• 25 acres of riparian and oak 

woodland habitat actively restored

• 65 acres of riparian and oak 

woodland habitat actively 

restored

• 65 acres allowed to restore 

through natural process 

restoration

N/A • 40 acres of riparian 

understory restored

• 25 acres of riparian 

understory restored

N/A • Establish a native plant 

nursery at HQ office

• No native plant nursery

N/A • Intensify control efforts for 

perennial pepperweed in 

riparian areas using a variety 

of methods

• Same as Alternative B

• Maintain existing fencing along 

SP Cut on the North Stone 

Lake Unit to exclude cattle from 

riparian areas

• Maintain and expand fencing 

along SP Cut on the North 

Stone Lake Unit to exclude 

cattle from riparian areas

• Same as Alternative A

Wetlands restoration 

and management

• 200 acres of wetland restored at 

Headquarters Unit

• Same as Alternative A • Same as Alternative A

• 452 acres of seasonal wetlands 

maintained

• 452 acres of seasonal 

wetlands manipulated 

to improve vegetation 

conditions

• 133 acres of seasonal 

wetlands manipulated 

to improve vegetation 

conditions

• 136 acres of vernal pool seasonal 

wetlands manipulated to improve 

vegetation conditions

• Same as Alternative A • Same as Alternative A

• 715 acres of permanent wetlands 

managed to provide habitat for 

a variety of wetland dependent 

species

• Same as Alternative A • Same as Alternative A

N/A • 50 acres wetlands enhanced 

on Beach Lake Unit

• Same as Alternative B

Grassland 

restoration and 

management

• 1,900 acres of non-irrigated 

grassland maintained and 

enhanced

• Same as Alternative A • Same as Alternative A

• 0 percent high residual dry matter • 20 percent high residual dry 

matter

• Same as Alternative B

Table 1. Summary of Alternatives
188 Stone Lakes NWR Comprehensive Conservation Plan

Alternative A Alternative B Alternative C

• Implement a long term grazing 

management plan developed 

in collaboration with range 

management experts

• Same as Alternative A • Same as Alternative A

• 0 acres planted to restore the 

native grassland community

• 30 acres planted to restore 

the native grassland 

community

• Same as Alternative B

N/A • Enhance and create habitat 

for burrowing owls by 

reintroducing ground 

squirrels to the North Stone 

Lake Unit and constructing 

and maintaining artificial 

burrows

N/A

Wet meadow/pasture 

management

• 460 acres of irrigated pasture/wet 

meadow maintained

• Same as Alternative A. • Same as Alternative A.

N/A • If feasible, sheet flood 

irrigated pastures to a depth 

of less than six inches every 

two weeks from November 

through March on the North 

Stone Lake Unit

• Same as Alternative B

N/A • Maintain grasslands by 

periodic disturbance (eg., 

mowing, grazing, burning, or 

discing)

• Same as Alternative B

Moist soil habitat 

management

• 529 acres of seasonal wetlands 

managed as moist soil habitat

• Same as Alternative A and: • Same as Alternative A but: 

• Flood moist soil units early Sept 

– May

• Same as Alternative A. • Begin floodup concurrent 

with first rainfall after Sept. 

1

• Stagger timing of drawdown 

starting in March

• Same as Alternative A. • Drawdown beginning in 

mid-March to mimic natural 

rainfall conditions

• Irrigate 1-2 times from May – Aug 

to promote desired vegetation

• Same as Alternative A • No irrigation from May 

- Aug

• Disc and/or mow 25-50% of units 

to stimulate plant growth and 

maintain equal ratio of open water 

to emergent vegetation

• Same as Alternative A • Same as Alternative A

N/A • Drawdown one permanant 

wetland in August to provide 

shorebird habitat and flood 

again in September with 

other wetlands

• Begin flooding seasonal 

wetlands concurrent with 

the first rainfall

Table 1. (continued)
Stone Lakes NWR Comprehensive Conservation Plan 189

Alternative A Alternative B Alternative C

N/A • Explore reverse cycle 

wetlands management on an 

experimental basis to benefit 

shorebirds

• Same as Alternative B

Sandhill crane 

habitat management

• 2,500 acres of Refuge lands 

managed to support a population 

of 400 to 700 sandhill cranes

• 2,950 acres of Refuge 

lands managed to support 

a population of 400 to 700 

sandhill cranes

• 2,700 acres of Refuge 

lands managed to support 

a population of 400 to 700 

sandhill cranes

N/A • Periodically sheet-flood 

irrigated pastures on North 

Stone Lake Unit in winter

• Same as Alternative B

N/A • Maintain 40 to 60 acres of 

agriculture fields (eg., corn, 

winter wheat and other small 

grains) on the Headquarters 

Unit of the Refuge for 

foraging cranes 

• Same as Alternative

Pest control • Use integrated pest management 

techniques to control weeds

• Same as Alternative • Same as Alternative A

• Continue cooperative water 

hyacinth control efforts

• Survey for and control 

Brazilian elodea

• Same as Alternative B

• Continue using prescribed fire, 

where appropriate

• Depending on restrictions, 

employ prescribed burns 

to reduce nonnative annual 

grasses and replicate the 

historical fire regime

• Same as Alternative B

• Drawdown managed permanent 

wetlands every two to four years 

to control carp populations and 

improve germination of desirable 

wetland plants

• Same as Alternative A • Same as Alternative A

N/A • Cooperate with other entities 

to conduct weed control

• Same as Alternative B

Hydrology 

management

Water Quality • Develop a long-term water quality 

monitoring plan

• Same as Alternative A and: • Same as Alternative B

N/A • Within 10 years of CCP 

approval, work toward 

achieving the water quality 

supply standard set forth by 

the USEPA, CDFG and the 

RWQCB

• Same as Alternative B

Table 1. (continued)
190 Stone Lakes NWR Comprehensive Conservation Plan

Alternative A Alternative B Alternative C

N/A • Develop a water quality 

monitoring program to track 

contaminant concentrations, 

and water quality 

parameters resulting from 

current and future land use 

patterns around the Refuge 

within five years

• Same as Alternative B

N/A • Develop strategies to 

educate local landowners, 

businesses, and 

neighborhood organizations 

within the watershed about 

nonpoint sources of pollution

• Same as Alternative B

N/A • Expand outreach and 

education effort to inform 

upstream urban residents 

and businesses about the 

sensitivity of downstream 

water uses

• Same as Alternative B

Floodplain 

management

• Manage Refuge floodplain in a 

manner consistent with regional 

water quality objectives, as 

described in the EIS establishing 

the Refuge

• Same as Alternative A • Same as Alternative A

N/A • Develop Refuge levee 

and flood control channel 

maintenance program

• Same as Alternative B

Visitor Use

Visitors • 3,000 wildlife observation visits 

per year

• 10,500 wildlife observation 

visits per year

• 15,000 wildlife observation 

visits per year

Trails • One trail • 4.0 miles of foot trails open to 

the public 7 days a week with 

seasonal restrictions

• 6.0 miles of foot trails open 

to the public 7 days a week 

with seasonal restrictions

N/A • 2.0 miles of universally 

accessible trail to be 

constructed on the 

Headquarters Unit and 

named the Blue Heron Trails 

System

• 2.5 miles of universally 

accessible trail to be 

constructed on the 

Headquarters Unit and 

named the Blue Heron 

Trails System

N/A 200 feet of boardwalk 

on Headquarters unit as 

part of the Blue Heron 

Trails System

• • 140 feet of boardwalk on 

Headquarters unit as part 

of the Blue Heron Trails 

System

N/A • 40 vehicle parking capacity 

on Headquarters unit

• 40 vehicle parking capacity 

on Headquarters unit

Table 1. (continued)
Stone Lakes NWR Comprehensive Conservation Plan 191

Alternative A Alternative B Alternative C

N/A • 1.5 miles of foot trails to be 

constructed on the South 

Stone Lake unit open to the 

public seven days a week 

with seasonal restrictions

• Same as Alternative B

N/A • 200 feet of boardwalk to be 

constructed on the South 

Stone Lake Unit open to the 

public seven days a week 

with seasonal restrictions

• Same as Alternative B

N/A • Develop a boat-accessible 

haul-out site, walking trail, 

and viewing blind on the 

South Stone Lake Unit 

• Same as Alternative B

N/A • Provide parking and 

boat launch capacity for 

approximately 10 cartop 

boats on the Beach Lake unit

• Same as Alternative B

N/A • Restrict land-based visitor 

use near habitat suitable 

for heron/egret rookeries, 

nesting Swainson’s hawks, 

and other areas used by 

nesting migratory birds 

during sensitive periods

• Same as Alternative B

N/A • Minimize disturbance to 

sandhill crane habitats by 

restricting public access 

during October through 

March

• Same as Alternative B

N/A • Reduce potential spread of 

invasive species by visitors 

by restricting access to 

paved or graveled trails 

• Same as Alternative B

N/A N/A • Develop two mile trail 

system on Beach Lake and 

North Stone Lake tracts to 

be open to the public seven 

days a week, with seasonal 

closures, and improve 

associated parking

N/A N/A • Resolve access issues and 

develop a parking area for 

five to ten cars and walking 

trails on Lodi Gun Club

Hunting • The 912-acre South Stone Lake 

Unit open to waterfowl hunting 

for up to 22 hunters, 2-3 days per 

week

• Same as Alternative A • Same as Alternative A

Table 1. (continued)
192 Stone Lakes NWR Comprehensive Conservation Plan

Alternative A Alternative B Alternative C

Fishing • No legal fishing • Within five years provide 

safe, boat-only fishing with 

day use parking facilities to 

accommodate approximately 

20 boats on South Stone 

Lake and approximately ten 

boats on SP Cut from June 

through September

• Same as Alternative B

N/A • Fishing will be in accordance 

with all State regulations, 

will not include take of frogs 

or crayfish and will only be 

done with rod and reel

• Same as Alternative B

Wildlife Viewing and 

Photography

N/A • Minimum of two 

photography blinds to be 

constructed 

• Same as Alternative B

N/A • Construct a viewing platform 

on the Headquarters Unit 

• Same as Alternative B

N/A • Construct a vehicular access 

point, parking area for 15 

cars, a trail and a wildlife 

observation platform on 

southern North Stone Lake 

Unit

• Same as Alternative B

N/A • Provide parking for 

approximately 20 cars at the 

boat launch on the South 

Stone Lake Unit 

• ame as Alternative B

Environmental 

Education and 

Interpretation

N/A • Develop a self-guided trail 

as part of the Blue Heron 

Trails System with hands-on 

learning stations within two 

years

• Same as Alternative B

N/A • Develop a class/group 

staging area and 5 open air 

interpretive shelters with 

one kiosk and exhibits as 

part of the Blue Heron Trails 

System to accommodate 

approximately 40 children

• Same as Alternative B

N/A • Develop interpretive displays 

on the Headquarters Unit 

to illustrate traditional 

dwellings, various 

subsistence strategies, and 

the overall lifestyle of local 

American Indians 

• Same as Alternative B

Table 1. (continued)
Stone Lakes NWR Comprehensive Conservation Plan 193

Alternative A Alternative B Alternative C

N/A • Develop self-guided trail and 

interpretive displays for the 

Wetland Preserve Unit

N/A

N/A N/A • Develop interpretive panels 

and exhibits on South Stone 

Lake Unit

Boating • High speed boating occurs as 

a non-sanctioned use, but has 

been allowed to continue pending 

compatibility determination. 

High speed boats (waterskiers) 

launch from off the refuge and ski 

through the Refuge.

• No-wake speed limit • Same as Alternative B

N/A • Develop and maintain a 

safe public parking lot and 

boat launch facilities to 

accommodate approximately 

20 cartop boats on the South 

Stone Lake Unit

• Same as Alternative B

N/A • Provide a launch for preregistered canoe/kayak 

groups in SP Cut on the 

Beach Lake Unit from June 

through September

• Same as Alternative B

N/A • Restrict water-based visitor 

use near habitat suitable for 

heron/egret rookeries and 

Swainson’s hawks during 

sensitive periods 

• Same as Alternative B

N/A • Develop facilities for mobility 

impaired persons to enter 

and exit canoes and kayaks

• Same as Alternative B

Cultural resources 

management

• Develop additional measures to 

protect, stabilize and/or remediate 

past damages if necessary

• Same as Alternative A and: • Same as Alternative B

• Meet annually with the Ione 

Band of Miwok Indians and 

other concerned tribal groups to 

discuss land management and 

restoration activities planned for 

the upcoming field season

• Within 15 years evaluate 

conditions of known cultural 

resource sites on Refuge 

managed lands and conduct 

seasonal monitoring of 

known sites

• Same as Alternative B

N/A • Develop a minimum of two 

interpretive panels and 

exhibits to be located on 

various units to share with 

the public the importance 

of cultural resources on the 

Refuge and American Indian 

cultural practices

• Same as Alternative B

Table 1. (continued)
194 Stone Lakes NWR Comprehensive Conservation Plan

Wetland Restoration

Natural Riparian ExpansionRiparian Restoration

Open WaterNon-Refuge LandsSeasonally Flooded

Figure 3. Habitat Management Alternatives

Sto

n

e

L

a

k

e

s

N

atio

n

al Wildlife

R

efu

g

e

Managed Wetlands

Unmanaged Wetlands &

Vernal Pools

Grasslands, Farmlands, &

Other

Riparian Forest

0 1 2 0.5 Miles

0 1 2 0.5

Kilometers

Alternative C

Alternative B

Alternative A

PasturesIrrigatedJuly-Oct

Restore 200 acof wetlands

-Promote growth of

waterfowl food plants

-Maintain ratio of open

water to emergent veg

-Control aquatic &

terrestrial weeds

-Control carp population

Expand riparian zoneFlood up in fallfor sandhill cranesand other waterbirdsDrawdown 1 unitin Aug for shorebirds

Periodicallyflood irrigatedpasturesNov-Marchas habitat formigratorywaterbirds

Flood up in fallfor sandhill cranesand shorebirdsManage grazingto provide foraging& loafing habitatfor sandhill cranesEstablish nativeplant nursery

Maintain/expandfencing toexclude cattlefrom riparianzone

Create/enhanceburrowing owlhabitat

Expand & restorecottonwood forest

Expand riparian zoneRestore upland veg

Flood upconcurrentwith 1st rainFlood upconcurrentwith 1st rainPassiverestoration ofriparian zoneManage grazingto provide foraging& loafing habitatfor sandhill cranesPassiverestoration ofriparian zone

Periodicallyflood irrigatedpasturesNov-Marchas habitat formigratorywaterbirds

Management in Alt A is also

applied in Alt B and C
Stone Lakes NWR Comprehensive Conservation Plan

 195

Stone Lakes

National Wildlife Refuge

Wildlife ObservationPhoto Blind or Platform

Waterfowl HuntingNon-Motorized Boating

Car-Top Boat Launch Boat Fishing Non-Refuge Lands

Grasslands, Farmlands & OtherWetlands & Vernal PoolsRiparian ForestOpen Water

Wetland Restoration

Seasonal Closure

Alternative B Alternative C Alternative A

Figure 4. Visitor Use Alternatives

Refuge Headquarters

Parking

Hiking Trails

1 0 1 0.5 Miles

1 0 1 0.5 Kilometers

Vernal PoolGuided ToursSchools & Other GroupsGuided Tours

Sandhill Crane ViewingObs BlindAccessibleby Boat

Trails, Boardwalk & Fishing1 Car Top Boat Launch

Trails & BoardwalksInterpretive Shelter & KioskCultural Resources DisplaysEnv. Ed Programs & StagingJr. Biologist Trail

Car Top Boat LaunchPre-Registered Persons/Groups

Open 2 days/monthHunting ProgramRefuge HeadquartersRestored Wetlands

Car/Top Boat LaunchPre-Registered Persons/Groups

TrailsJunior Biologist Trail

TrailsSandhill Crane Viewing

Vernal PoolGuided Tours

Trails, Boardwalk & Fishing1 Car Top Boat Launch

Trails & Obs BlindAccessible byBoat & Car

Trails & BoardwalksInterpretive Shelter & KioskCultural Resources Display

Visitor Services in Alt Aalso apply in Alt B and C
196 Stone Lakes NWR Comprehensive Conservation Plan

Vernal Pool Management

Vernal pools are present on the North Stone Lake and Wetland Preserve units. The 

Wetland Preserve Unit contains the highest concentration of vernal pools (98 percent of all 

Refuge vernal pools) that harbor the Federally-listed vernal pool fairy shrimp (Branchinecta 

lynchi) and vernal pool tadpole shrimp (Lepidurus packardi) and many vernal pool plant 

and animal species of concern (USFWS 2005). Only 12 percent of the vernal pools located on 

the Refuge are naturally occurring. The majority have been created over the last 15 years 

as mitigation for vernal pool loses elsewhere. 

Hunting

Through a separate planning process from the Refuge CCP, the Service has implemented a 

waterfowl hunting program on the Refuge that will remain in effect under all Alternatives. 

Currently, the program is offered two days per week on the South Stone Lake Unit and 

consists of seven spaced blinds, with an emphasis on youth and handicap hunters. Over 

the next five years, the program will expand to provide hunting opportunities for up to 22 

hunters. Hunting occurs currently only on the Sun River property of the South Stone Lake 

Unit but as more resources become available for the Refuge, the program will expand to 

include more of South Stone Lake. The Service currently emphasizes youth hunting by 

reserving at least two blinds for youth hunters and by providing two youth hunts before 

and after the waterfowl season in accordance with State regulations. Currently, the entire 

program is operated by the Refuge but the California Department of Fish and Game may 

assume a more active role, in cooperation with the Service, as hunting expands. 

Boating 

A number of private landowners with property adjacent to the Refuge have allowed access 

to waterways in the Stone Lakes Basin for a variety of different boating activities (e.g., 

waterskiing, fishing, waterfowl hunting). The Service has allowed boating to continue on 

Refuge waters within the Beach Lake and North Stone Lake units pending finalization 

of compatibility determinations for visitor uses. Under all alternatives, the Service will 

continue to allow some boating on the Refuge. 

Cultural Resources

To preserve and minimize disturbance to Refuge archaeological and historic resources, 

all undertakings, including but not limited to ground disturbance and prescribed burns, 

will be coordinated with the Service’s Regional Archaeologist. In consultation with the 

State Historic Preservation Office and local tribal representatives, the Service will ensure 

that Refuge activities comply with all relevant cultural resource protection laws, including 

Section 10 of the National Historic Preservation Act and the Native American Graves 

Protection and Repatriation Act. Any cultural resources overviews or site surveys for 

properties or monitoring of ground disturbing activities will be conducted by qualified 

professional archaeologists. The Refuge will continue to consult regularly with the Ione 

Band of Miwok Indians and other concerned tribal organizations on management and 

restoration projects, as well as plant-gathering activities and interpretive projects. 

Alternatives Removed From Further Consideration

Auto Tour Route on North Stone Lake Unit and Associated Trails

The Service considered creating an automobile tour route and associated walking trails 

on the North Stone Lake Unit. Developing an auto tour route was rejected because since 

the entire unit lies within the 100-year floodplain, accommodating vehicle traffic would 

necessitate construction of new roads involving major grading and gravel placement on a 

unit where preservation of natural topography and hydrology and native grass communities 

are management priorities. Furthermore, greater sandhill cranes (Grus canadensis tabida) 

and white-fronted geese use the area for foraging during winter and are highly sensitive 
Stone Lakes NWR Comprehensive Conservation Plan 197

to automobile and pedestrian traffic. An auto tour route would also further fragment the, 

already limited crane habitat on the Refuge. Walking trails and a viewing platform on the 

North Stone Lake Unit are still components of the alternatives considered in this CCP. 

Equestrian Use

After receiving inquiries from selected members of the public, the Service evaluated 

accommodation of equestrian use on the Refuge. However, this is considered a nonwildlife-dependent use and there are no trails suitable for riding that would not conflict 

with other priority visitor uses. Moreover, there are no adequate parking facilities for 

horse trailers and the Service determined that the limited parking areas available should be 

primarily for priority visitor uses such as wildlife observation and fishing that do not require 

trailers. Horses traveling through the Refuge may be a source for the introduction and 

spread of exotic and invasive plants . Many trails are primarily on levees and use by horses, 

particularly after precipitation, could accelerate the erosion of these levees. Other nearby 

areas have more extensive horse trails and are better able to accommodate horse use. These 

areas include the American River Parkway and Auburn State Recreation Area. 

Upland Game and Deer Hunting

Refuge Staff considered the inclusion of upland game and deer hunting in formulating the 

alternatives. However, since such a program would be limited to land that the Service owns 

in fee (1,740 acres in four isolated areas; only two of which support upland habitat), not 

enough acreage is in Refuge ownership to provide quality, safe upland game or deer hunting 

with a reasonable chance of hunter success. If additional lands are added to the Refuge, 

upland game and deer hunting could be reconsidered.

Fishing Derbies

Some of the public suggested the Service consider fishing derbies on the South Stone 

Lake Unit. Fishing derbies typically involve fast moving, gas powered boats that conflict 

with other non-motorized boats, such as canoes or kayaks, used for wildlife observation. 

Furthermore, South Stone Lake is a small body of water with underwater hazards and 

dense, submerged vegetation and is too small for a quality fish derby. Other nearby 

locations, such as reservoirs, are better suited for this activity.

Alternative A: No Action

Under this alternative, the Service would continue to manage Stone Lakes Refuge as it 

has in the recent past. Management would be consistent with the “Current Management” 

section in Chapter 3 of the CCP. Current staffing and funding needs would remain the same.

Habitat Restoration

Under this alternative, the 330-acre Headquarters Unit would be restored primarily to 

wetland habitat (200 acres), with 50 acres of native grassland habitat and 80 acres of farmed 

land. 

Migratory Birds

Flood up, drawdown and summer irrigations will continue to be scheduled to provide 

habitat for migrating, wintering and breeding birds. These actions will occur on 840 acres 

of wetlands, 360 acres of riparian habitat, 3,320 acres of grassland habitat, 400 acres of open 

water/aquatic bed habitat, 460 acres of irrigated pasture and 305 acres of cropland. Seasonal 

wetlands will be managed to provide feeding and loafing habitat for wintering migratory 

waterbirds. Water would continue to be carefully managed to produce food and to create 

habitat for nesting waterbirds. The Service would continue to maintain water through most 

of the summer in permanent wetlands to provide rearing habitat for waterbirds and yearround habitat for other species, such as bitterns, herons and marsh wrens (Cistothorus
198 Stone Lakes NWR Comprehensive Conservation Plan

palustris). Drawdowns will continue to vary to stimulate production of a variety of plants 

and to provide habitat for nesting shorebirds. Wildlife friendly farming practices would be 

continued to supply grain and other forage for birds on about 320 acres.

Monitoring

The Service would continue its ongoing monitoring programs, including colonial waterbird 

nesting, landbird, song sparrow, weekly waterfowl, plant, noxious weed and residual dry 

matter (dry grass remaining after the growing season) surveys.

Special Status Species

Sandhill crane. Under this alternative, the Service would continue to manage the Refuge 

to benefit sandhill cranes by managing 460 acres of irrigated pasture, 540 acres of seasonally 

flooded wetlands, 305 acres of cropland, and 3,320 acres of grassland habitat. 

Swainson’s hawk. The Refuge would continue to provide breeding and foraging habitat for 

Swainson’s hawks (Buteo swainsoni). However, there would be no increase in these habitats 

since no additional acres of riparian, grassland, or wetland habitat would be restored.

Valley elderberry longhorn beetle (VELB). Although there are no documented 

occurrences of the Valley Elderberry Longhorn Beetle (Desmocerus californicus 

dimorphus, VELB) on the Refuge, suitable VELB habitat is present on the Refuge. All 

existing elderberry shrubs (Sambucus sp.), the host plant for the VELB, are mapped. 

Shrubs that may be affected by the water hyacinth control program are monitored during 

the water hyacinth control season to minimize disturbance during water hyacinth control 

operations. 

Giant garter snake. The most recent documented occurrence of the giant garter snake 

(Thamnophis gigas) on the Refuge was in 1992 at Beach Lake. Recent surveys have not 

located any, although the snake is presumed to be present on the Refuge. Aside from 

avoidance, no specific measures have been taken to manage for the snake.

Wetland, Grassland, Riparian Habitats

Wetlands would continue to be managed for the benefit of migratory birds. Wetlands (moist 

soil units) would be flooded from September to May for the benefit of migratory waterbirds. 

Grassland habitat would continue to be mowed and grazed. Grazing would occur on about 

1,900 acres of the Refuge on the North Stone Lake Unit. No attempts to restore native 

grassland would be pursued. The Service would continue to allow researchers to conduct 

research on the Refuge but would not actively encourage or support research.

The Service would continue to manage the existing riparian habitat and would continue, 

sporadically, to plant riparian vegetation up to one mile from the edge of the SP Cut and 

adjacent to lakes on the Refuge where soils are appropriate and as time and funding allow. 

Little or no active riparian restoration would occur. 

New Lands

Additional lands within the approved Refuge boundary that come under Refuge 

management would be evaluated and either maintained in agriculture beneficial to wildlife or 

developed into natural habitats, such as wetlands, grasslands and riparian areas, depending 

on site-specific conditions.

Visitor Services

Under alternative A, the Refuge visitor services program would continue as described 

under “Visitor Services” in Chapter 3 of the CCP. The Refuge would continue its current 
Stone Lakes NWR Comprehensive Conservation Plan 199

wildlife observation and photography program, limited to two Refuge tour days per month. 

Environmental education would not change on the Refuge. Twenty-five groups would 

continue to visit the Refuge at their current level, with a limited number of presentations 

by Refuge staff at schools, public service and conservation group meetings. The Refuge 

would continue to host Walk on the Wildside, an annual special event held on the Refuge. 

The Refuge would continue to offer a waterfowl hunting program on the South Stone Lake 

Unit. Sixteen hunters would be accommodated two days a week. Under this alternative, 

an emphasis would be placed on youth and disabled hunters. In addition to blinds reserved 

for youth and disabled hunters, the Refuge would hold two youth hunts before the hunting 

season and two after the season.

Alternative B

Alternative B is the preferred alternative because it meets the criteria described in the 

Proposed Action Criteria section at the end of this chapter. Under Alternative B, the Refuge 

would continue its current focus of providing wintering habitat for migratory birds and 

management for the benefit of special status species. Management programs for migratory 

birds and other Central Valley wildlife would be expanded and improved, as described below. 

Visitor use opportunities would also be expanded as described below. 

Habitat Restoration

Alternative B would include the same elements as Alternative A. The Service would also 

restore Refuge lands based on the habitat requirements of migratory birds and special 

status species, which includes 65 acres of riparian habitat, 40 acres of wetland habitat and 30 

acres of native grassland habitat. 

Migratory Birds

Alternative B would include the same elements as Alternative A. Additional riparian and 

seasonal and permanent wetlands would be restored. Measures would be implemented 

to increase the food supply and provide additional migratory bird habitat, such as sheet 

flooding irrigated pastures, habitat manipulations, grazing to promote native grasses and 

forbs and exploring reverse-cycle wetland regimes. Reverse-cycle wetlands are flooded 

during the spring/summer and are dry during the fall/winter. Additional coordination is 

planned with other agencies and nongovernmental organizations under Alternative B. 

Visitor use would be restricted during heron and Swainson’s hawk nesting and sandhill 

crane roosting. A portion of South Stone Lake would also be closed to boating seasonally to 

protect nesting waterbirds and giant garter snake habitat.

Monitoring

Under this alternative, monitoring would be the same as for alternative A. In addition, the 

Service would monitor wetland, riparian and oak woodland habitats each spring for invasive 

species, such as cocklebur, yellow starthistle and perennial pepperweed. The Service would 

develop a Refuge water-quality monitoring program, expand migratory bird monitoring and 

develop surveys on the South Stone Lake, Headquarters, Wetlands Preserve units and other 

lands as they come under Refuge management.

The Service would continue to collaborate with Sacramento-Yolo Mosquito Vector Control 

District (SYMVCD) on the ongoing landbird monitoring program and pursue funding for 

a seasonal employee or graduate students to assist with the banding program and data 

analysis to assess population trends and assist with developing associated habitat restoration 

and management plans. This expansion is not included in Alternative C.
200 Stone Lakes NWR Comprehensive Conservation Plan

Special Status Species

Sandhill crane. Under this alternative, the Service would continue to manage for cranes 

as in Alternative A. In addition, there would be an increase of 80 acres of foraging and 

resting habitat with 50 acres of wetland and 30 acres of native grasslands habitat restored. 

In addition, when possible, Refuge staff would begin flooding moist soil units in early 

September to provide shallow water for cranes earlier in the season.

Swainson’s hawk. Under this alternative, there would be an increase in 65 acres of 

breeding habitat since 65 additional acres of riparian habitat would be restored. In addition, 

30 acres of native grassland would be restored, adding to existing foraging habitat. 

Valley elderberry longhorn beetle (VELB). The Refuge would continue to map and 

monitor elderberry shrubs as in Alternative A. In addition, the Service would restore 40 

acres of riparian understory, to include elderberry shrubs, which would benefit the VELB.

Giant garter snake. Same as Alternative A.

Wetland, Grassland, and Riparian Habitats

Wetland habitat would be expanded on 50 acres of the South Stone Lake Unit. The Service 

would use the same tools and techniques to manage wetland units under Alternative B as 

it does under Alternative A. However, some fields would be flooded in early September 

to provide habitat for cranes earlier in the year. Under Alternative B, seasonal marsh 

management activities would be the same as described under Alternative A. In addition, one 

permanent wetland unit would be drawn down in August to provide habitat for migrating 

shorebirds. Vernal pools on the Wetland Preserve Unit would be grazed. 

Portions of the Beach Lake, North Stone Lake, and South Stone Lake units would be closed 

as a sanctuary. The Lewis property of the Beach lake Unit and the Wetland Preserve and 

portions of the Headquarters units would be subject to seasonal closure to provide wildlife 

sanctuaries. 

Grassland habitat would be restored on 30 acres. For this alternative only, burrowing owl 

habitat would be improved by reintroducing ground squirrels (Spermophilus beecheyi) 

and constructing artificial burrows. Irrigated pasture would be grazed from July through 

October to promote native grasses and forbs and shortgrass conditions.

Riparian habitat would be expanded along lower Morrison Creek on the Beach Lake Unit, 

the south arm of North Stone Lake and the Sacramento drainage canal and South Stone 

Lake on the Headquarters and South Stone Lake units. In addition, riparian habitat would 

be managed for a variety of different successional stages for the benefit of neotropical 

migrants, colonial nesting birds and raptors.

New Lands. 

Same as alternative A.

Visitor Services 

Visitor Services would be improved and expanded under alternative B. For example, the 

number of units open to visitors would increase from one to five. In addition, environmental 

education, interpretation, wildlife observation, wildlife photography, hunting and fishing 

programs would be expanded, as described below. Visitor Services would be offered on the 

South Stone Lake, Headquarters, Beach Lake, Wetland Preserve and North Stone Lake 

units. The South Stone Lake, Headquarters, and a portion of North Stone Lake units would 

be open to visitors seven days a week from sunrise until sundown.
Stone Lakes NWR Comprehensive Conservation Plan 201

Visitor services would be concentrated south of Hood-Franklin Road at the Headquarters 

and South Stone Lake Units. A trail system with boardwalks, interpretive displays, 

parking for 40 cars and an environmental education center would be constructed on the 

Headquarters Unit. A trail system and observation platform overlooking South Stone Lake 

would be constructed. The environmental education and interpretive programs would be 

facilitated by Refuge staff or volunteers.

A boat launching area would be provided on the Sun River property of the South Stone Lake 

Unit for fishing, wildlife observation and photography from boats. Only non-motorized, 

hand-launched boats (e.g., canoes, kayaks) or non-trailered boats with electric motors 

would be allowed. A no-wake zone with boat speeds of less than five mph will be enforced 

for all Refuge waters. All fishing would be from boats only. A boat haul-out site would 

be constructed on the Lodi Unit upstream from Sun River. Non-motorized boating by 

pre-registered groups, including commercial outfitters who engage in fishing, and wildlife 

observation, would also be allowed on SP Cut on the Beach Lake and North Stone Lake 

units at the west end of Elliott Ranch Road. 

Safe access to the North Stone Lake Unit would be constructed to a parking area for 25 

cars on the north side of Hood-Franklin Road. A short trail would lead to an observation 

platform overlooking North Stone Lake to provide visitors an opportunity to view sandhill 

cranes and other wildlife. Schools and other groups would use the Beach Lake Unit for 

guided tours only. 

The Wetland Preserve Unit would be open to the visitors for guided tours and via a selfguided trail. 

The volunteer and outreach programs would expand and become more defined. 

The hunt program would be the same as alternative A.

Other major new visitor services projects under this alternative include: developing new 

interpretive signs, displays and interpretive brochures for the Wetland Preserve and 

Headquarters units; and constructing and making accessible on a daily basis, a kiosk, 

boardwalk, and four miles of walking trails on the Headquarters Unit; and constructing two 

photo blinds and additional hunting blinds on the South Stone Lake Unit.

Alternative C

Under this alternative, the Service would continue to focus on providing wintering habitat 

for migratory birds and managing for endangered species while placing a greater emphasis 

on historic conditions in management and habitat restoration activities as described below. 

Opportunities for the six priority public uses would be expanded from both alternatives A 

and B.

Habitat Restoration

Management of newly acquired Refuge lands would focus on the restoration of historic 

native plant communities rather than maintaining lands in agriculture or constructing 

wetlands. Under this alternative, 40 acres of riparian, 25 acres of understory shrub, 50 acres 

of wetland and 30 acres of native grassland habitat would be restored.

Migratory Birds

Alternative C would be similar to alternative B, however, more emphasis would be placed 

on restoration of natural conditions. Riparian restoration would be accomplished by natural 

process restoration. Flood up would not occur in early September as in alternatives A and 

B, but would begin with the first rainfall. 
202 Stone Lakes NWR Comprehensive Conservation Plan

Monitoring

Same as Alternative B, except that there would be no expansion of the SYMVCD 

monitoring.

Special Status Species

Sandhill crane. Same as alternative B.

Swainson’s hawk. Same as alternative B, except that restored breeding habitat would be 

increased by 40, rather than 65, acres. Restored foraging habitat would remain the same as 

in Alternative B.

Valley elderberry longhorn beetle (VELB). Same as alternative B, except with fewer 

acres of riparian understory shrubs planted. In alternative B, 40 acres of shrubs would be 

restored; under alternative C shrub habitat would increase naturally by approximately 25 

acres.

Giant garter snake. Same as Alternative A.

Wetland, Grassland, Riparian Habitats

Grassland and wetland habitat will be restored as in alternative B. Although seasonal 

wetlands would still be managed to provide feeding and loafing habitat for waterbirds, they 

would not be managed as intensely as the moist soil units in alternatives A and B. would In 

addition, flood-up for seasonal wetlands would begin with the first rainfall in fall rather than 

beginning in early September.

Riparian habitat restoration would be through natural process-based restoration only. 

Vegetation would not be planted, but would be allowed to expand naturally. In addition, 

the Service would allow riparian habitat to expand naturally into managed seasonal and 

permanent wetland units.

New Lands

Under this alternative, new lands brought under the protection of the Refuge System would 

be restored to historic conditions, where feasible. Restoring new lands to natural historic 

conditions would probably result in restoration of grassland habitat and to a lesser extent, 

wetland and riparian habitats. By contrast, alternatives A and B would likely result in more 

wetland habitat than grassland habitat.

Visitor Services

Under this alternative, visitor service facilities would be expanded as in alternative B. In 

addition, the Beach Lake Unit would be open to visitors seven days a week from sunrise to 

sunset, subject to seasonal closure.

Visitor Services provided at the Headquarters Unit would be similar. However, the 

environmental education and interpretive programs would de-emphasize programs 

facilitated by Refuge staff or volunteers and tours would be self-guided.

Visitor services for the South Stone Lake Unit would be similar to those offered in 

Alternative B. In addition to the facilities for South Stone Lake described in Alternative B, 

the Service would create vehicle access to a parking area for up to ten cars. The parking 

area would be connected to the trail system.

Visitor services for the north side of Hood-Franklin Road would be the same as Alternative 

B.
Stone Lakes NWR Comprehensive Conservation Plan 203

In addition to the guided tours and canoe and kayak groups described in Alternative B, 

visitor services concentrated in the Beach Lake Unit would include environmental education, 

interpretation, wildlife observation and photography. The parking area near the corral on 

the North Stone Lake Unit would be improved and include restrooms, trails, interpretive 

displays, and an environmental education kiosk. 

Visitor services for the Wetland Preserve Unit would be the same as alternative B.

The hunt program would be the same as alternative A.

The volunteer and outreach programs would be the same as alternative B.

Proposed Action Criteria

The planning policy that implements the Improvement Act of 1997 requires the Service to 

select a preferred alternative that becomes its proposed action, as required by the NEPA. 

The written description of this proposed action is effectively the draft CCP. Alternative B is 

the proposed action for the Refuge because it best meets the following criteria:

• achieves the mission of the National Wildlife Refuge System;

• achieves the purposes of the Refuge;

• provides guidance for achieving the Refuge’s 15 year vision and goals;

• maintains and restores the ecological integrity of the habitats and populations on the 

Refuge;

• addresses the important issues identified during the scoping process;

• addresses the legal mandates of the Service and the Refuge; and

• is consistent with the scientific principles of sound fish and wildlife management and 

endangered species recovery.

The proposed action described in this EA is preliminary. The action ultimately selected and 

described in the final CCP will be determined, in part, by the comments received on this 

version of the EA. The proposed action presented in the final CCP may or may not be the 

preferred alternative presented in this version. The final CCP may propose a modification 

of one of the alternatives presented here or a combination of elements from more then one 

alternative. Alternative B is the preferred alternative.
204 Stone Lakes NWR Comprehensive Conservation Plan

Chapter 3. Affected Environment

Chapter 3 of the CCP provides a detailed description of the affected environment for Stone 

Lakes National Wildlife Refuge.
Stone Lakes NWR Comprehensive Conservation Plan 205

Chapter 4. Environmental Consequences

Overview of the NEPA Analysis Parameters

This chapter describes the direct, indirect and cumulative impacts of the three alternatives. 

The purpose of this analysis is to provide the context and intensity of the impacts of each 

action, such that a determination of significance can be made by the deciding official.

In 1978, the Council on Environmental Quality promulgated regulations for implementing 

the NEPA. These regulations include a definition of significantly as used in the NEPA (40 

CFR 1508.27). The elements of this definition are critical to reducing paperwork through 

use of a Finding of No Significant Impact (FONSI) when an action will not have a significant 

effect on the human environment and is therefore exempt from requirements to prepare an 

environmental impact statement (EIS). Human environment is a comprehensive phrase that 

includes the physical and natural environments and the relationship of people with those 

environments. Many of the analyses focus on the different resource areas such as soils, air 

quality, water quality, plant communities, wildlife, visitor services and others. It is important 

to note that for each of these criteria all of these resources, or human environments, have 

been considered.

The significance of an action must be analyzed in several contexts, such as the whole of 

society; affected region; affected interests and locality. Significance varies with the setting. 

In the case of a site-specific action, significance would usually depend on the effects in the 

locale rather than in the world as a whole. Both short- and long-term effects are relevant. 

The regional context of the action alternatives is the Beach–Stone Lakes Basin. Even in a 

local context, the action alternatives would not pose significant short- or long-term effects. 

The action alternatives are designed to minimize and avoid adverse impacts to the extent 

that such impacts are less than significant, even a the local level. 

Alternative A, the No Action Alternative, is a continuation of current management practices; 

it serves as the baseline against which Alternatives B and C are compared. Discussion of 

the action alternatives, Alternatives B and C, follow each discussion of No Action. 

Soils

Common to all Alternatives. Under all alternatives the Refuge would continue to use, 

Service-approved aquatic herbicides, such as Aquamaster and Remedy and terrestrial 

herbicides such as Roundup and 2, 4-D, for weed control. Glyphosate, the active ingredient 

in Aquamaster and Roundup, is considered nonmobile in soils and sediments because 

it rapidly and strongly adheres to soil particles and degrades in the soil. Glyphosate is 

moderately persistent in the soil, with an estimated half-life of 47 days. Glyphosate has 

no known effect on soil microorganisms. The World Health Organization (1984) concluded 

that 2, 4-D does not accumulate or persist in the environment. The primary degradation 

mechanism is microbial metabolism, but mineralization and possibly photolysis may also 

play a role. The average half-life of 2, 4-D is ten days (Tu, M. et al 2001). 

Alternative A. Under Alternative A, the Service would complete construction of wetlands 

and grasslands on the Headquarters Unit and would redesign the Headquarters entrance; 

as described in a previous draft environmental assessment (EA), issued March 4, 2005. 

Construction activities could result in large areas of bare soil that could be subject to 

erosion. Erosion is expected to be minor and localized because construction will occur only 

during the dry season, the terrain is flat and the Refuge will employ dust control measures. 
206 Stone Lakes NWR Comprehensive Conservation Plan

Alternative B. In addition to the potential soil impacts related to construction on the 

Headquarters Unit, Alternative B could also result in similar impacts due to restoration 

activities, including restoration or enhancement of 105 acres of riparian and oak woodland 

habitat, 30 acres of grasslands and 50 acres of wetlands. Developing visitor facilities on the 

South Stone Lake, Headquarters, North Stone Lake, Beach Lake and Wetland Preserve 

Units could result in impacts, as well. These impacts are expected to be minor and localized 

for the same reasons described above. Additional short-term disturbance would result 

from mechanical removal of nonnative weeds from the seasonal marsh, riparian and upland 

habitats.

Alternative C. In addition to the soil impacts described under Alternative B, Alternative 

C also includes other Refuge improvements that could result in the same type of impacts. 

These improvements include natural process-based restoration of 65 acres of riparian 

habitat in addition to the same construction, weed removal and wetland and grassland 

restoration as in Alternative B. 

Water Quantity and Quality

Common to all Alternatives. Under all alternatives, the conversion of 200 acres of former 

agricultural lands on the Headquarters Unit to wetlands would add to the region’s 

floodwater storage capacity and help maintain water quality by trapping sediments and 

removing some excess nutrients. 

Alternative A. No impacts on water quality or quantity are anticipated under Alternative 

A. Under all alternatives, glyphosate will be used in the form of Roundup and Aquamaster 

to control aquatic and terrestrial weeds. In most cases, glyphosate will dissipate rapidly 

from natural water bodies through adsorption to organic substances and inorganic clays, 

degradation and dilution (Folmar et al. 1979, Feng et al. 1990). 

Alternatives B and C. Under Alternatives B and C, periodic flooding of irrigated pastures 

would begin earlier each fall, adding to groundwater recharge. The restoration and natural 

expansion of riparian vegetation would help to stabilize shorelines; this would reduce 

erosion and the resulting sediment loads in Refuge waters, improving water quality. The 

prohibition of gas-powered boats within the Refuge under Alternatives B and C would 

contribute to better water quality by removing a source of turbidity, potential petroleum 

leaks and inadvertently transported aquatic nuisance species. As new lands come under 

Refuge management and are either converted from agricultural uses or removed from urban 

development pressures, further benefits to water quality would accrue through reductions in 

erosion, sedimentation and nonpoint source pollution.

Air Quality

Alternative A. Under all alternatives, soil disturbance and/or use of heavy equipment 

would cause short-term increases in dust (particulate matter less than 10 microns [PM10]) 

and tailpipe emissions of PM10, nitrogen oxide (NOX) and reactive organic gasses (ROG), 

including those activities associated with the restoration of wetland habitat on the 

Headquarters Unit. However, implementation of Alternative A (No Action Alternative) 

would not substantially increase pollutant emissions related to Refuge management in the 

long term. Since no increase in the level of visitor services is proposed, visitor use levels 

and vehicle trips to and from the Refuge are expected to increase only moderately as the 

population of the surrounding region grows. 

Alternatives B and C. In addition to the short-term impacts to air quality from wetland 

restoration on the Headquarters Unit, under Alternatives B and C, there would be both 

short and long-term increases in pollutant emissions. Short-term increases in PM10 and 
Stone Lakes NWR Comprehensive Conservation Plan 207

tailpipe PM10, NOX and ROG would result from restoring riparian habitat on the North 

Stone Lake, Headquarters, and South Stone Lake units and constructing trails, parking 

areas and observation platforms. Tailpipe emissions (ROG, NOX, and PM10) would result 

from the use of combustion engines in construction equipment and employee vehicles during 

trips to and from the job sites. Dust emissions and generation (PM10) would result from the 

excavation, transport and grading of large amounts of soil.

Long-term increases in emissions would result from the growing number of vehicular trips 

to, from and on the Refuge as visitation increases. This increase is expected to be similar 

under both action alternatives, at about 10,500 to 15,000 more visitors per year by 2012. 

However, there would be a slight decrease in emissions from gasoline powered boats since 

only non-motorized and electric motor boats would be allowed.

Plant Communities

Common to all Alternatives. Discing, mowing, chemical treatments, and occasionally 

grazing would be periodically used to maintain cover of emergent vegetation in seasonal 

wetland impoundments at 45-55 percent of total wetland surface area. The Service would 

continue to use physical and chemical means to control undesirable plants such as cocklebur 

and joint grass. These same techniques would be used to manage vegetation in about 

25 percent of the moist soil impoundments each year to reduce the cover of emergent 

vegetation and encourage the growth of annuals that provide food for waterfowl, maintaining 

an equal ratio of open water to emergent vegetation. The Service would continue to mow 

and graze grassland habitat to reduce the cover of non-native annual grasses and promote 

native species.

All applications of aquatic herbicides (e.g., glyphosphate, diquate dibromide) will be from 

properly calibrated and maintained ground or boat-mounted spray apparatus. In keeping 

with product labels, no applications will occur when wind speeds exceed 10 miles per 

hour. All applications will occur in compliance with best management practices identified 

in the Aquatic Pesticide Application Plan for the Statewide National Pollution Discharge 

Elimination System (NPDES) General Permit (No. CAG990005) for discharge of aquatic 

pesticides administered by the Central Valley Regional Water Quality Control Board. 

Alternative A. Under Alternative A (no action), current vegetation management would 

continue unchanged. Wetlands would be flooded from early September through May for 

the benefit of migratory waterbirds and would continue to be mowed, grazed, disced and 

sprayed with pesticides. In addition, under all alternatives, the Service would maintain 

360 acres of riparian and oak woodland habitat, 529 acres of moist soil seasonal wetlands, 

136 acres of vernal pool seasonal wetlands, 715 acres of permanent wetlands, 460 acres of 

irrigated pasture/wet meadow and restore 25 acres of riparian habitat on the Headquarters 

Unit.

Alternative B. Alternative B would include the same vegetation management measures 

as described under Alternative A. In addition, the Service would increase the cover of 

native seasonal marsh plants on the Refuge by controlling nonnative weeds. In addition, 

the Service would restore 65 acres of riparian and oak woodland habitat, along the North 

Stone Lake, Headquarters and South Stone Lake units, as well as enhancing 40 acres of 

understory shrub and herbaceous vegetation in existing riparian areas. Planting riparian 

vegetation and restoring seasonal wetland and grassland habitat would have a beneficial 

effect on local and regional biodiversity because the vast majority of the historic riparian 

vegetation in the Central Valley has been lost or degraded. Under both Alternatives B and 

C, 30 acres would be planted to restore native grasslands throughout the Refuge. This 

would have a beneficial effect on the Refuge’s vegetation because it would restore a larger 

diversity of the Refuge’s native plant cover. 
208 Stone Lakes NWR Comprehensive Conservation Plan

Enhancement and restoration of native grasslands, wetlands, and riparian habitats on the 

Refuge would not exacerbate threats of weed infestations to adjacent properties because 

Refuge staff and cooperators would continue to promote desirable vegetation and control 

invasive weeds as part of ongoing management programs. Some weed species of concern 

that will require ongoing control include: perennial pepperweed or whitetop, yellow star 

thistle, Johnson grass, and fennel or anise. Control of invasive weeds would be part of an 

integrated pest management program that would include physical (e.g., mowing, discing, 

grazing, and burning) and chemical (herbicide) treatments.

Alternative C. Impacts under Alternative C would be similar to those described under 

Alternative B, with a few differences. Riparian habitat expansion would be allowed to 

proceed through natural succession and volunteering by riparian woody species. There 

would be no active planting of riparian vegetation. However, riparian vegetation would be 

allowed to expand into wetland habitat on the Beach Lake and South Stone Lake units. 

Under Alternative C, the Service would restore 65 acres of riparian vegetation as under 

Alternative B. This would have a beneficial effect on the Refuge’s vegetation because it 

would restore a larger diversity of the Refuge’s native plant cover. 

Wildlife

Common to all Alternatives. Under all alternatives, the Service would continue to allow 

the Sacramento Yolo Mosquito Vector Control District (SYMVCD) to monitor and control 

mosquitoes on the Refuge. The typical monitoring and control period is March through 

October. The mosquito species identified by SYMVCD for monitoring and control at the 

Refuge are Culex tarsalis, Anopheles freeborni, Aedes vexans, Aedes melanimon, Aedes 

nigromaculis, and Aedes increpitus. The SYMVCD would use the biological larvicides 

Bacillus thuringiensis isrealensis (Bti) and Bacillus sphaericus (Bsp) and the insect growth 

inhibitor methoprene. The bacterium Bti is a microbial insecticide that, when ingested, 

is toxic to mosquitoes, black flies and several other members of the Nematocera suborder 

within the order Diptera. Methoprene is an insect growth regulator that interferes with 

the normal maturation process of mosquitoes. In the event, adulticide applications become 

necessay, SYMVCD will utilize synthetic pyrethrins or the organophosphate Naled, applied 

from an ultra-low volume ground rig. 

See Appendix L, Integrated Pest Management Plan for Mosquito-Associated Threats 

and Appendix A, Compatibility Determination, Use: Monitor and Control Mosquitoes, for 

detailed descriptions of mosquito control on the Refuge and the potential impacts to target 

and non-target organisms.

Under all alternatives, control of invasive weeds, particularly aquatic weeds such as 

water hyacinth, currently require the application of herbicides (i.e., Diquat dibromide and 

Glyphosate). Glyphosate has low acute toxicity, is not a carcinogen, does not adversely 

affect reproduction and development, and does not bioaccumulate (build up) in mammals 

(Monsanto 2001). When applied properly, Glyphosate is of relatively low toxicity to birds, 

mammals and fish (Evans and Batty 1986). However, amphibians may potentially be 

negatively affected by Glyphosate that enters aquatic systems (Smith 2001).

All alternatives identify herbicide use to control invasive terrestrial or aquatic weeds. 

Glyphosate and Diquat dibromide herbicides could have short-term negative effects on 

aquatic wildlife and waterbirds, but removal of invasive weeds favors native plants and 

ultimately improves the quality of wildlife habitat. Refuge staff will continue to comply 

with National Pollution Discharge Elimination System general permit protocols and best 

management practices for aquatic herbicide applications and water quality monitoring 

that were developed by the Central Valley Regional Water Quality Control Board to avoid 
Stone Lakes NWR Comprehensive Conservation Plan 209

adverse effects on water quality and aquatic wildlife. Glyphosate, found in both Roundup® 

and Rodeo®, does not bioaccumulate in fish. The Rodeo® formulation is practically nontoxic to freshwater fish and aquatic invertebrates, while the Roundup® formulation is 

moderately to slightly toxic to freshwater fish and aquatic invertebrate animals. However, 

in laboratory studies, Roundup® has been shown to cause high rates of mortality to juvenile 

North American tadpoles (Relyea 2005). Clopyralid is of low toxicity to fish, aquatic 

invertebrate animals, birds, and mammals, is not toxic to bees and has very low acute 

mammalian toxicity. It does not bioaccumulate in fish. Triclopyr is low in toxicity to fish, 

does not bioaccumulate in fish, and is slightly toxic or nontoxic to invertebrates; however, 

it has not been tested for chronic effects in aquatic animals. Triclopyr is slightly toxic to 

mammals, however, in mammals, most triclopyr is excreted unchanged in urine. Triclopyr 

and its formulations have very low toxicity to birds and is nontoxic to bees. Sethoxydim 

is practically nontoxic to birds, has low toxicity to wildlife, and is nontoxic to bees. It is 

moderately to slightly toxic to aquatic species. Only herbicides that are approved for use 

near water, such as Rodeo®, Reward ®, or Garlon 3a®, would be used on Refuge lands that 

are within 100 feet of surface waters. In addition, to prevent further water contamination 

and effects to aquatic species, the Refuge would not spray when wind velocities exceed five 

miles per hour, when vegetation is wet, or when precipitation is occurring or forecasted in 

the following 24 to 36 hours. Herbicide applications are not expected to significantly affect 

wildlife.

Some negative effects to reproductive success of late-nesting ground nesting birds, such as 

mallards (Anas platyrhynchos), and meadowlarks may occur during prescribed fires and 

mowing operations

Alternative A. Under Alternative A, current management of the Refuge would continue 

unchanged. The Refuge would continue to manage water for migratory waterfowl, 

shorebirds, water birds and other migratory birds. Grasslands and agricultural lands would 

continue to be managed to provide foraging and loafing habitat. Under this alternative, no 

new riparian or wetland habitat would be restored or created beyond the restoration of 25 

acres of riparian habitat on the headquarters unit, but existing habitat would be maintained 

and fostered. Maintaining and fostering habitat would benefit the variety of wildlife that 

uses the Refuge, including birds of prey, songbirds, waterfowl and colonial nesting birds, 

such as egrets and herons as well as many species of mammals and reptiles.. 

Because visitor use is currently limited to bimonthly tour days and hunting for 16 hunters 

two days per week during waterfowl season, human disturbance to wildlife would be minimal 

under Alternative A. By contrast, Alternatives B and C both would increase visitor use and 

implement a recreational fishing program. Potential impacts of visitor use include: flushing 

of birds, disruption of feeding and roosting activity, reducing use of preferred habitat, and 

increasing bioenergetic demands (DeLong 2002). 

Alternative B. Alternative B would result in mostly beneficial and some adverse impacts 

on wildlife. Recreational use of the Refuge is expected to increase dramatically under 

Alternative B. Most of these new users are expected to participate in wildlife observation. 

This growth in recreational use could adversely affect birds using the Refuge wetlands, 

resulting in flushing, disruption of feeding and roosting, increased demands on the birds’ 

available energy and reduced use of preferred habitat (DeLong 2002). 

Under Alternative B, visitor use facilities such as parking areas, kiosks, trails and new 

buildings would be developed. This could result in the temporary disturbance and/or 

displacement of wildlife due to construction activities. The riparian portion of the unit 

would not be directly affected by construction but wildlife would, nonetheless, experience 
210 Stone Lakes NWR Comprehensive Conservation Plan

disruption because of the nearby construction activity. Once construction is completed, 

substantial numbers of waterfowl, shorebirds and other waterbirds would be expected to 

utilize the restored and enhanced wetlands of the Headquarters Unit. 

Sixty-five acres of riparian vegetation would be restored throughout the Refuge, an 

additional 40 acres of riparian understory vegetation would be enhanced, 50 acres of 

wetlands near South Stone Lake would be enhanced and planting native grasses over 30 

acres in various portions of the Refuge would begin. Once established, this new habitat 

would provide a long-term benefit to a variety of wildlife, including migratory songbirds and 

birds of prey. In addition, existing grassland habitat would be maintained through grazing, 

mowing and/or burning for the benefit of grassland dependent species. Riparian habitat 

would be further protected by further exclusion of cattle from riparian areas. Shorebirds 

would benefit from exploring reverse-cycle wetlands and by drawing down one permanent 

wetland until August to provide food. The Refuge would also enhance and create habitat 

for burrowing owls by reintroducing ground squirrels to the North Stone Lake and Wetland 

Preserve units and constructing artificial burrows, as needed. 

Under Alternative B, the Refuge would be opened to fishing from non-motorized, handlaunched boats (e.g., canoes, kayaks) or non-trailered boats with electric motors only. A 

boat launching area would be provided on the Sun River property of the South Stone Lake 

Unit Non-motorized boating by pre-registered groups, including commercial outfitters who 

engage in fishing, and wildlife observation, would also be allowed on SP Cut on the Beach 

Lake and North Stone Lake units at the west end of Elliott Ranch Road. 

No native game fishes remain in Refuge waters but introduced game fish species are 

abundant, so the direct impact of recreational fishing on fish populations is not expected to 

be detrimental. Fishing may even benefit native fish species by reducing habitat competition 

from introduced species. Indirect effects of fishing and boating, such as disturbance to 

waterfowl, reptiles and amphibians, would be controlled by restricting shoreline fishing, 

by allowing access only during the summer before winter migrants have arrived and by 

providing sanctuary to species that are present during the summer. 

Alternative C. Alternative C would result in primarily beneficial impacts on wildlife and 

few adverse impacts. The effects on wildlife under this alternative would be similar to those 

described under Alternative B, with the following exceptions.

Implementation of Alternative C would have similar effects on the Headquarters Unit 

as would Alternative B. Under this alternative, riparian vegetation would be allowed to 

expand naturally into managed wetland units. Though some riparian restoration along 

North Stone Lake would occur, no new riparian restoration would take place in the Sun 

River, Headquarters or Beach Lake units. The more limited and gradual increase in 

riparian habitat would still benefit wildlife over a longer period than under Alternative B. 

The reduction in wetland restoration and construction under Alternative C would result 

in reduced disturbance for wildlife. The effects on wildlife from the hunting and fishing 

programs are similar to Alternative B. 

Special Status Species

Suitable habitat exists on the Refuge for the federal ESA listed giant garter snake, valley 

elderberry longhorn beetle (VELB), vernal pool tadpole shrimp and fairy shrimp . Vernal 

pool tadpole and fairy shrimp are the only federal ESA listed species whose presence has 

been verified on the Refuge within the last 13 years. California Endangered Species Act 

listed species that inhabit the Refuge include greater sandhill crane and Swainson’s hawk. 
Stone Lakes NWR Comprehensive Conservation Plan 211

Alternative A. Under Alternative A, continuation of current management activities will 

have beneficial effects on special status species. The Service will continue to manage 

the Refuge to support sandhill cranes by providing irrigated pasture, seasonally flooded 

wetlands, grain crops and grasslands. Breeding and foraging habitat would also be provided 

for Swainson’s hawks in the Refuge’s riparian forests and grasslands. Though there are no 

documented occurrences of VELB on the Refuge, all existing elderberry shrubs are mapped 

and protected from herbicides intended to control invasive weeds.

Alternative B. No significant adverse effects on special status species are anticipated. 

Beneficial effects to special status species would result from expansion and enhancement 

of riparian, wetland and grassland habitats. However, increases in human disturbance due 

to the increased number of visitors may also occur. Human disturbance would most likely 

affect sandhill cranes and Swainson’s hawks. 

Swainson’s hawks would benefit from increased riparian habitat under Alternative B, 

including the expansion of riparian vegetation along the North Stone Lake, Headquarters, 

South Stone Lake, and Beach Lake units and the Sacramento Drainage Canal. Access for 

recreational fishing allowed between June and September could affect nesting Swainson’s 

hawks, because their nesting season typically lasts from mid-February through July. As a 

result, the Service will prohibit visitor access within a 0.25-mile radius of any occupied hawk 

nest until the young have fledged. 

Under Alternative B, the Refuge would enhance habitat management for sandhill cranes 

by flooding earlier in the fall (mid-September) than under Alternative A, by periodically 

flooding irrigated pastures and by developing a grazing program near North Stone Lake 

to provide foraging and loafing habitat adjacent to roosting sites. The Refuge also plans to 

construct a new observation platform for viewing sandhill cranes north of Hood Franklin 

Road on the North Stone Lake Unit. Alternative B’s net effect is expected to be beneficial 

for sandhill cranes because while visitor disturbance will increase, habitat will also increase 

and greater foraging opportunities will be available.

No impact to vernal pool species is anticipated under Alternative B. The majority of the 

vernal pools at the Refuge occur in the Wetland Preserve Unit. This area will be opened 

for guided tours and via a self-guided trail that will be routed to avoid impacts to wetlands. 

Therefore, visitor use is not expected to affect the vernal pool tadpole shrimp or fairy 

shrimp.

The VELB would benefit under Alternative B by planting early successional upland 

vegetation, including elderberry bushes, on the South Stone Lake Unit. Riparian and 

grassland restoration will also benefit the Swainson’s hawk.

Alternative C. The effects of Alternative C on special status species are largely the same 

as in Alternative B except that less riparian habitat would be restored. The Refuge would 

continue its sandhill crane habitat management as in Alternative B. The natural expansion 

of riparian vegetation allowed under Alternative C would ultimately benefit Swainson’s 

hawks.

Diseases and Toxins

Common to all Alternatives. Under each alternative, the Service would continue current 

botulism control practices, including keeping all units dry between June 1 and August 1; 

patrolling historically problematic wetlands on the Refuges and in the surrounding areas 

in cooperation with the California Department of Fish and Game; and removing sick birds 

and carcasses from wetlands. As a result of these coordinated activities, the potential for an 

outbreak of botulism would be minimized. 
212 Stone Lakes NWR Comprehensive Conservation Plan

Increased wetland habitat under Alternative B, increases the potential for breeding 

mosquitoes and hence, could lead to an incremental increase in the potential spread of 

mosquito-borne diseases. In accordance with their 1993 Memorandum of Understanding, 

Refuge staff will continue efforts to minimize mosquitoes in cooperation with SYMVCD 

through wetland design, efficient water management, vegetation manipulations through 

mowing, discing, and burning, biological control such as planting of mosquitofish, 

and applying larvicides and adulticides, as needed. See Appendix L, Integrated Pest 

Management Plan for Mosquito-Associated Threats for a detailed description of mosquito 

control on the Refuge.

Under all alternatives, the Service would continue to prohibit lead shot for waterfowl 

hunting as it has been Refuge system policy for over 15 years. 

Cultural Resources

Common to all Alternatives. Under all alternatives, including the No Action alternative, 

Refuge management activities have the potential to disturb cultural resources. To preserve 

Refuge archaeological and historic resources, all undertakings, including but not limited to 

ground disturbance and prescribed burns, will be coordinated with the Service’s Regional 

Archaeologist. Under each alternative: a cultural resources overview would be prepared; 

baseline data on all cultural resource sites collected; an attempt made to locate and delineate 

all unrecorded cultural resource sites; appropriate buffers zones established to ensure their 

protection; and updated or new site records forwarded to the California North Central 

Information Center. Also, an attempt would be made to locate any human remains, covered 

under the Native American Grave Protection and Repatriation Act (NAGPRA) (25 USC 

3001 et seq. or 43 CFR 10), removed in the past from within the Refuge boundary 

When it is determined after consultation with the Service’s Regional Archaeologist and 

local professional archaeologists, that a consultation with the State Historic Preservation 

Office (SHPO) under Section 10 of the National Historic Preservation Act is warranted for a 

planned undertaking, the Refuge will ensure that appropriate procedures to protect cultural 

resources and provide necessary mitigation are identified and implemented, in accordance 

with the Service Programmatic Agreement for cultural resources with the SHPO. All 

monitoring of ground-disturbance will be performed by a professional archaeologist who 

may request assistance from tribal representatives. The Refuge will provide copies of SHPO 

correspondence and monitoring reports to the Regional Archaeologist and any concerned 

tribal organizations. 

A cultural resources survey may not be required if burning is proposed entirely within a 

flood zone, in a previously disced or plowed area, or if burning has been an ongoing practice 

on the site. However, cultural resources surveys will likely be necessary for all burns 

on upland sites, and for burns that require excavation (scraping, plowing, or discing) to 

establish a fire line. In some cases, it may be appropriate to conduct cultural resources 

survey work after a prescribed burn is completed, because the visibility of artifacts or 

other resources may be increased after burning and artifacts may be more vulnerable to 

vandalism or theft when exposed by burning. 

As required by the NAGPRA, any construction or ground-disturbing activity with the 

potential to disturb human remains, burial objects, sacred objects, or objects of cultural 

patrimony will be planned and implemented in consultation with affected Tribes. If 

potentially significant artifacts are found during any activity, work will cease within 100 feet 

of the find and access will be restricted until a qualified archaeologist and members of local 

Tribes can assess the significance of the find and propose appropriate methods of treatment, 

as required by NAGPRA. If human remains are found during any activity, work will cease 
Stone Lakes NWR Comprehensive Conservation Plan 213

within 100 feet of the find, access will be restricted and the Sacramento County Coroner will 

be informed of the discovery, as required under Public Resources Code Section 5050.5. If no 

investigation of the cause of death is required, remains will be treated in accordance with the 

requirements of NAGPRA.

With assistance from the Service’s Regional Archaeologist and local professional 

archaeologists, the Refuge has identified the Ione Band of Miwok Indians as the nearest 

tribal organization with whom the Refuge should consult on management and restoration 

projects. As a result, the Refuge intends to meet with the tribal liaison at least annually to 

discuss any planned project that may result in ground disturbance of prehistoric or historic 

sites. 

Visitor Services

According to California State Department of Finance projections, the population of the 

Delta Region (Sacramento, Solano, Yolo, San Joaquin and Contra Costa Counties) is 

expected to grow by about 19 percent between 2005 and 2020. The State as a whole is 

expected to grow by 24 percent over the same period. In the western states, participation 

in hunting is predicted to decline by 21 percent in the period between 1995 and 2020. For 

example, statewide hunter use days declined in four out of five years, through 2004 (USFWS 

2004). The trend for non-consumptive recreation shows an opposite trend. Participation 

in non-consumptive recreation is expected to increase by 37 percent over the same period 

(Cordell et al. 1999). 

Common to All Alternatives. Under each alternative, hunting on the South Stone Lake 

Unit is expected to continue at 16 hunters per day, for two days per week throughout the 

hunt season, with two youth only hunts held both before and after the regular hunt season. 

Non-consumptive recreation will increase at a rate proportional to the predicted population 

growth for the five county Delta/Sacramento metropolitan region. Currently, Stone Lakes 

receives about 3,500 visits per year consisting of 3,000 wildlife observation visitors and 25 

environmental education groups of 20 each. 

 

Alternative A. Under the No Action alternative, the Refuge is expected to receive 4,200 

visits annually by 2020. This projected increase in visitor use under the no action alternative 

serves as a baseline against which to compare the action alternatives. Figure 5 shows the 

current visitor use levels and predicted use levels under each alternative. Under the No 

Action alternative, the Service would maintain current Refuge visitor services and facilities. 

However, overall Refuge use is expected to increase as the population of the Sacramento 

metropolitan area and the rest of the State continues to grow over the next 15 years. 

Alternative B. Visitor services would be improved and expanded under Alternative B. 

Volunteer opportunities would be expanded, including at least one comprehensive volunteer 

training per year. Opportunities for wildlife observations would expand to a capacity of 

10,500 visits per year. Four miles of foot trails would be open to visitors seven days a week, 

with seasonal restrictions. Two miles of universally accessible trails would be constructed 

on the Headquarters Unit and named the Blue Heron Trails System. Two new photography 

blinds would be constructed, on the North Stone Lake and Headquarters Units. Two 

hundred feet of boardwalk, on the Headquarters Unit, would be constructed as part of the 

Blue Heron Trails System. One and one-half miles on foot trails would be constructed on 

the South Stone Lake Unit and would be open to visitors seven days a week, with seasonal 

restrictions. Two hundred feet of boardwalk would be constructed on the South Stone 

Lake Unit and would be open to visitors seven days a week, with seasonal restrictions. 

Parking facilities and a car top boat launch, for a maximum of ten cars, would be provided 

on the Beach Lake Unit. The number of supported environmental education groups would 
214 Stone Lakes NWR Comprehensive Conservation Plan

expand to 80 per year. Two new interpretative programs would be developed within five 

years, including displays illustrating traditional dwelling and subsistence strategies on the 

Headquarter Unit. 

Within five years the Refuge would provide safe, boat only fishing with day use parking 

facilities that could accommodate up to 20 boats per day. Refuge staff would expand 

community outreach and would expand the number of presentations given to schools, 

conservation groups and public service organizations. 

Figure 5. Current and Projected Visitation (15 years).

Alternative C. Under this alternative, visitor service facilities would be similarly expanded 

as in Alternative B. Opportunities for wildlife observations would expand to a capacity of 

15,000 visitors per year. Six miles of foot trails would be open to visitors seven days a week, 

with seasonal restrictions. Less boardwalk would be constructed at the Headquarters Unit 

(140 feet). An additional two miles of trails would be developed on the Beach Lake and 

North Stone Lakes Units and would be open to visitors seven days a week, with seasonal 

closures. Four new interpretative programs would be developed within the next five years. 

Socioeconomics

It is well known that Americans value recreational opportunities, although there is no 

general agreement on the best methodology to precisely measure the impact of recreational 

opportunities on local economies. Recreational use of the Refuge probably has indirect 

economic benefits to the local community, although given the limited resources available for 

the production of the draft CCP/EA, no formal economic study of these benefits has been 

conducted. However, it is probable that local use of Refuge recreational opportunities will 

approximate National trends to the extent that the uses are allowed on the Refuge. 

As determined by a Compatibility Determination (see Appendix A), high-speed boating 

conflicts with paddle-based recreation (ex. canoeing, kayaking and fishing from nonmotorized boats) and limits visitor services that can be offered on the Refuge. Many other 

proposed Refuge uses, that water skiing and high speed boating are incompatible with, are 
Stone Lakes NWR Comprehensive Conservation Plan 215

actually more popular than water skiing nationally. According to USA Waterski, there are 

approximately 11 million water skiers in the U.S. (USA Waterski 2006). According to the 

Outdoor Industry Foundation other proposed Refuge visitor services enjoy much larger 

national popularity (see Figure 6) including: hunting at 12,800,000 participants, paddle-based 

recreation at 23,596,000 participants, fishing at 32,900,000 participants and wildlife viewing 

at 66,100,000 participants (OIF 2006). 

National Trends for Proposed Active Recreational Uses

11,000,000

12,800,000

23,596,000

66,100,000

32,900,000

Water Skiing

Hunting

Paddle-Based Recreation

Wildlife Viewing

Fishing

As noted in a letter from the Beach Lake Ski Club dated October 23, 2006 (see Appendix G, 

Response to Public Comments) currently a private water ski club, consisting of 23 families, 

uses Refuge waterways for high speed boating for approximately four months each year. 

The water ski club estimates that weekly usage varies from a low of 8 families (boats) per 

week to a high of 12 families per week or an average of 10 families per week during the ski 

season. If high speed boating is discontinued on the Refuge, then other conflicting uses 

such as paddle-based recreation and wildlife observation and photography can increase as 

proposed, in the preferred alternative, by Objective 3.B. of the draft CCP. 

Alternative A. Under the No Action alternative, current management practices would 

continue to be followed and no change in Refuge staffing would be required. Under the 

No Action Alternative, there would also be no change in visitor services and no changes in 

the indirect costs or benefits associated with visitor services to the local economy. The No 

Action alternative would thus have no impact on local employment conditions or the local 

economy.

Alternatives B and C. Actions proposed under Alternatives B and C are expected to have no 

significant affect on the local, regional or State economy. Under the preferred alternative, 

high speed boating will be phased out and several other uses, that high speed boating 

conflicts with, will be allowed to increase. Increases in Refuge visitation for activities such 

as wildlife observation and photography, environmental education and interpretation and 

recreational boating are expected under the preferred alternative.

Visitor services on the Refuge probably benefit the local economy and employment 

Figure 6. National Outdoor Recreation Totals for 2006.
216 Stone Lakes NWR Comprehensive Conservation Plan

conditions when Refuge visitors purchase goods from local businesses, such as gas stations, 

restaurants, hotels, photography stores, and sporting good stores. Under the preferred 

alternative, there will likely be a loss of benefits to local businesses from patronage by high 

speed boaters, but there will likely be a simultaneous gain in benefits for local businesses 

from added patronage by increasing numbers of other Refuge visitors. Actions proposed 

under Alternatives B and C are thus expected to have modest net benefits to the local 

economy once only uses found to be compatible are allowed on the Refuge. Table 2 displays 

the proposed net increases in Refuge visitor services, under Alternatives B and C.

The proposed expansion in visitor services programs may lead to increases in Refuge 

budget and staffing. Additional funding and staff proposals related to implementation of the 

CCP will be entered into the Service’s agency budget systems, including Refuge Operating 

Needs System and Maintenance Management System. Additional Refuge staff required 

under these alternatives may be hired from local communities and would likely live in and 

contribute to the local communities.

Action

Estimated Annual Refuge 

Visitation

Annual Number of 

People Visiting

Annual Number of 

Families Visiting 

Average Water Skiing Use 532 160

Wildlife Observation 3,000 901

Environmental Education 315 95

Hunting 315 95

Total Annual Use - 

Alternative A 4,162 1,251

Average Water Skiing Use 0 0

Wildlife Observation 10,500 3,153

Environmental Education 1,050 315

Hunting 315 95

Total Annual Use - 

Alternative B 11,865 3,563

Increase from the No Action 

Alternative 7,703 2,312

Average Water Skiing Use 0 0

Wildlife Observation 15,000 4,505

Environmental Education 1,050 315

Hunting 315 95

Total Annual Use - 

Alternative C 16,365 4,914

Increase from the No Action 

Alternative 12,203 3,663

Alternative A Alternative B Alternative C

As incompatible high speed boating is phased out, the local water skiing club, would be 

expected to lose benefits associated with this temporal, exclusive use of Refuge waters and 

to incur costs associated with finding alternative water skiing locations if they choose to do 

so. The loss of benefits would be due to the water ski club’s contractual obligation, until 2013 

Table 2. Estimated Visitor Services on the Refuge Under Alternatives A, B, and C. ** The 

average family size in Sacramento County is 3.33 persons (ACS 2004).
Stone Lakes NWR Comprehensive Conservation Plan 217

(see letter from the Beach Lake Ski Club dated October 23, 2006), with a local landowner 

for the use of launch facilities that provides access to a waterway, partially located on the 

Refuge. A local fishing club, that uses gas powered boats, also uses launch facilities provided 

by the same land owner. Since the Refuge has no authority to regulate high speed boating 

outside of Refuge boundaries, only a portion of the water course regularly water skied and 

fished via gas-powered boats will be lost to high speed boating as will commensurate benefits 

associated with access to those parts of the waterway. However, it is unclear if the parts 

of the waterway outside of the Refuge boundary would be considered viable for continued 

water skiing, by the club. If the local water ski club could not continue to water ski, within 

the waterway outside of the Refuge boundary, then the preferred alternative would result 

in a total loss of benefits associated with the use of the waterway. The private fishing club 

could continue to fish throughout the waterway, however without the use of high-speed boats. 

So there could be a small opportunity cost to the fishing club as travel times within Refuge 

waterways are increased, without the use of high speed boats.

If the water ski club finds that the waterway outside of the Refuge boundary is not viable for 

water skiing and therefore chooses not to renew a contract with the local land owner, who 

provides launch facilities, then the local land owner would incur opportunity costs after 2013 

unless the local landowner substituted another profitable use of the property. 

The expanded wildlife-dependent visitor use opportunities proposed under Alternatives 

B and C could result in increased instances of trespass, vandalism, and littering and some 

minor disruption of farming practices of adjacent to nearby landowners.

No projects proposed under any of the alternatives would have a disproportionate negative 

impact on low-income or minority populations.
218 Stone Lakes NWR Comprehensive Conservation Plan

Appendix 1: References 

Boisvert, M., and J. Boisvert. 2000. Effects of Bacillus thuringiensis var. israelensis

on target and nontarget organisms: a review of laboratory and field experiments. 

Biocontrol Science and Technology 10: 517-561.

Breaud, T.P., J.E. Farlow, C.D. Steelman, and P.E. Schilling. 1977. Effects of the insect 

growth regulator methoprene on natural populations of aquatic organisms in Louisiana 

intermediate marsh habitats. Mosquito News. 37(4): 704-712.

California Department of Fish and Game (DFG). 2000. The status of rare, threatened, 

and endangered animals and plants of California, Annual Report for 2000. California 

Department of Fish and Game. Sacramento, CA. 226 pp.

California Department of Fish and Game (DFG). 2006. California Wildlife: Conservation 

Challenges (California’s Wildlife Action Plan). Prepared by Bunn, David, Andrea 

Mummert, Roxie Anderson, Kirsten Gilardi, Marc Hoshovsky, Sandra Shanks and 

Kiffanie Stahle. Wildlife Health Center, University of California, Davis.

Charbonneau, C.S., R.D. Drobney, and C.F. Rabeni. 1994. Effects of Bacillus thuringiensis 

var. israelensis on nontarget benthic organisms in a lentic habitat and factors affecting 

the efficacy of the larvicide. Environmental Toxicology and Chemistry 13 Vol. 2:267-

279.

Cordell, H.K., C, Betz, J.M. Bowker, and others. 1999. Outdoor recreation in American 

life: a national assessment of demand and supply trends. Sagamore Publishing, 

Champaign, IL. 219-321. 

Dale, P.E.R. and K. Hulsman. 1990. A critical review of salt marsh management methods 

for mosquito control. Crit. Rev. in Aquatic Science 3:281–311.

DeLong, A.K. 2002. Managing visitor use and disturbance of water birds–a literature 

review of impacts and mitigation measures–prepared for Stillwater National Wildlife 

Refuge. Stillwater National Wildlife Refuge Complex final environmental impact 

statement for the comprehensive conservation plan and boundary revision (Vol. II), 

Appendix L. Department of the Interior, U.S. Fish and Wildlife Service, Portland, OR. 

114 pp.

Extension Toxicology Network (ETN). 1996. Naled Pesticide information profile. 

http://ace.ace.orst.edu/info/extoxnet/pips/naled.htm

Euliss, N.H., and S.W. Harris. 1987. Feeding ecology of northern pintails and green-winged 

teal wintering in California. Journal of Wildlife Managment 51: 724-732.

Evans, D.D., and M.J. Batty. 1986. Effects of high dietary concentrations of glyphosate 

on a species of bird, marsupial and rodent indigenous to Australia. Environmental 

toxicology and chemistry 5: 399-401.

Feng, J.C., D.G. Thompson, and P.E. Reynolds. 1990. Fate of glyphosate in a Canadian 

forest watershed: 1. Aquatic residues and off-target deposit assessment. Journal of 

Agricultural Food Chemistry 38: 1110-1118.
Stone Lakes NWR Comprehensive Conservation Plan 219

Folmar, L.C., H.O. Sanders, and A.M. Julin. 1979. Toxicity of the herbicide glyphosate 

and several of its formulations to fish and aquatic invertebrates. Archives of 

Environmental Contamination and Toxicology 8: 269-278.

Hansen, G.W., F.E. Oliver, and N.E. Otto. 1984. Herbicide manual. A Water Resources 

Technical Publication. U.S. Department of the Interior, Bureau of Reclamentation, 

Denver, CO. 346 pp.

Heady, H. F. 1977. Valley grassland. P ages 491-514 In M. G. Barbour and J. Major, eds.

Terrestrial vegetation of California. John Wiley and Sons, New York.

Lacey, L.A., and M.S. Mulla. 1990. Safety of Bacillus thuringiensis var. israelensis and 

Bacillus sphaericus to non-target organisms in the aquatic environment. In Laird, M., 

L.A. Lacey, E.W. Davidson, editors. Safety of microbial insecticides. CRC Press.

Merritt, R.W., E.D. Walker, M.A. Wilzbach, K.W. Cummins, and W.T. Morgan. 1989. A 

broad evaluation of Bti for black fly (Diptera: Simuliidae) control in a Michigan 

River: efficacy, carry and nontarget effects on invertebrates and fish. Journal of the 

American Mosquito Control Association 5: 397-415.

Miura, T., and R.M. Takahashi. 1974. Insect developmental inhibitors. Effects of candidate 

mosquito control agents on nontarget aquatic organisms. Environmental Entomology 

3: 631-636.

Miura, T., and R.M. Takahashi. 1973. Insect developmental inhibitors. Effects on nontarget 

organisms. Journal of Economic Entomology 66: 917-922.

Monsanto. 2001. Aquamaster Technical Fact Sheet. 

Niemi, G.J., A.E. Hershey, L. Shannon, J.M. Hanowski, A. Lima, R.P. Axler, and R.R. Regal. 

1999. Ecological Effects of Mosquito Control on Zooplankton, Insects, and Birds. 

Environmental Toxicology and Chemistry 18(3): 549-559.

Norland, R.L., and M.S. Mulla. 1975. Impact of Altosid on selected members of an aquatic 

ecosystem. Environmental Entomology 4: 145-152.

Outdoor Industry Foundation (OIF). 2006. The Active Outdoor Recreation Economy. 

Relyea, Rick A. 2005. The Lethal Impact of Roundup on Aquatic and Terrestrial 

Amphibians. Ecological Applications: 15 (4): 1118–1124.

Riparian Habitat Joint Venture (RHJV). 2004. Version 2.0. The Riparian Bird Conservation

Plan: a Strategy for Reversing the Decline of Riparian Associated Birds in California. 

California Partners in Flight. http://www.prbo.org/calpif/pdfs/riparian.v-2.pdf.

Smith, G.R. 2001. Effects of Acute Exposure to a Commercial Formulation of Glyphosate 

on the Tadpoles of Two Species of Anurans. Bulletin of Environmental Contaminant 

Toxicology: 67(4): 483-488.

State of California, Department of Finance. 2001. Interim County population projections. 

Sacramento, California, June 2001.

Stebbins, G. Ledyard. 1965. Colonizing species of the native California flora. In The 

Genetics of Colonizing Species. Academic Press, NY, pp. 173-191.
220 Stone Lakes NWR Comprehensive Conservation Plan

Thomas, C.M., and T.C. Maurer. 2003. Toxicity of Stormwater Runoff at Stone Lakes 

National Wildlife Refuge, 1999-2000, Final Report, Investigation No.: 199910003, U.S. 

Department of the Interior, Fish and Wildlife Service, Portland, Oregon.

Tomlin, C. 1994. The Pesticide Manual. Farnham: British Crop Protection Council/

Cambridge: Royal Society of Chemistry.

Tu, M., C. Hurd, and J.M. Randall. 2001. Weed Control Methods Handbook, The Nature 

Conservancy, http://tncweeds.ucdavis.edu version: April 2001.

USA Waterski. 2006. USA Water Ski Profile.

http://www.usawaterski.org/pages/USA-WS%20Profile.htm

Viewed on December 8, 2006.

U.S. Fish and Wildlife Service (USFWS). 1992. Environmental impact statement with 

appendices for Stone Lakes National Wildlife Refuge Project, Sacramento County, 

California; Final. With technical assistance provided by Jones & Stokes Associates, 

Inc. (JSA 91-047). Sacramento, CA.

U.S. Fish and Wildlife Service (USFWS). 2004. Kern and Pixley National Wildlife Refuges 

Comprehensive Conservation Plan. Sacramento, CA. 

U.S. Fish and Wildlife Service (USFWS). 2005. Recovery Plan for Vernal Pool Ecosystems 

of California and Southern Oregon. Portland, OR.

http://www.fws.gov/sacramento/es/recovery_plans/vp_recovery_plan_links.htm

World Health Organization. 1984. 2,4-Dichlorophenoxyacetic acid (2,4-D), Environmental 

Health Criteria 29. United Nations Environment Programme, Geneva. 151 pp.

Personal Communications

Ivey, G. 2002. Wildlife and Habitat Review. 

Marty, J. 2004. The Nature Conservancy (TNC). September, 2004.

Van Loben Sels, R. 2005. Subject. RD 744.

G. Geupel, Point Reyes Bird Observatory (PRBO). 2004.
Stone Lakes NWR Comprehensive Conservation Plan 221

Appendix C. Wildlife Species Found on Stone 

Lakes National Wildlife Refuge

Stone Lakes NWR Reptiles

Common Name Scientific Name Habitat Sp S F W

Class AMPHIBIA (amphibians) 

Order Anura

Family BUFONIDAE (true toads)

western toad Bufo boreas msrg r r r r

Family HYLIDAE (tree frogs and relatives)

pacific treefrog Pseudacris regilla rm c c c r

Family RANIDAE (true frogs)

bullfrog Rana catesbeiana omr c c c r

Class REPTILIA (reptiles) 

Order SQUAMATA (lizards and snakes)

Family ANGUIDAE (alligator lizards and relatives)

southern alligator lizard Elgaria multicarinata rg r r r r

Family COLUBRIDAE (Colubrids)

western yellowbelly racer Coluber constrictor 

mormon 

rg u c u r

common kingsnake Lampropeltis getula sg u c u r

gopher snake Pituophis catenifer sg u c u r

elegant garter snake Thamnophis elegans sm u c u r

giant garter snake Thamnophis gigas msrg r r r r

common garter snake Thamnophis sirtalis sm u c u r

Family PHRYNOSOMATIDAE (North American spiny lizards) 

western fence lizard Sceloporus occidentalis sg c c c c

Order TESTUDINES (turtles) 

Family EMYDIDAE (box and water turtles)

western pond turtle Clemmys marmorata (syn.

Emys marmorata) 

om u u u r

red-eared slider Trachemys scripta om u u u u
222 Stone Lakes NWR Comprehensive Conservation Plan

Stone Lakes NWR Mammals 

Common Name Scientific Name Habitat Sp S F W

Order ARTIODACTYLA (even-toed hoofed animals)

Family CERVIDAE (deer, moose, reindeer, elk)

black-tailed deer Odocoileus hemionus rsg r r r r

Order CARNIVORA (meat-eaters)

Family CANIDAE (coyotes, dogs, foxes, jackals and wolves)

coyote Canis latrans wide c c c c

gray fox Urocyon 

cinereoargenteus

gr o o o o

Family FELIDAE (cats)

feral house cat Felis catus rgu c c c c

Family MEPHITIDAE (skunks and stink badgers)

striped skunk Mephitis mephitis wide u u u u

Family MUSTELIDAE (badgers, otters, weasels and relatives)

river otter Lontra canadensis or c c c c

mink Mustela vison om o o o o

Family PROCYONIDAE (coatis, raccoons, lesser pandas)

raccoon Procyon lotor mr c c c c

Order CHIROPTERA (bats)

Family MOLOSSIDAE (free-tailed bats)

guano bat Tadarida brasiliensis r r r r r

Order DIDELPHIMORPHIA (American marsupials)

Family DIDELPHIDAE (opossums)

virginia opossum Didelphis virgiana r c c c c

Order INSECTIVORA (insect-eaters)

Family Soricidae (shrews)

ornate shrew Sorex ornatus msg r r r r

Order LAGOMORPHA (pikas, hares and rabbits)

Family LEPORIDAE (hares and rabbits)

black-tailed jackrabbit Lepus californicus sg c c c c

desert cottontail Sylvilagus audubonii g c c c c

Order RODENTIA (gnawing mammals)

Family CASTORIDAE (beavers)

beaver Castor canadensis mr a a a a

Family CRICETIDAE (New World rats and mice, voles, hamsters and relatives)

California vole Microtus californicus gr c c c c

muskrat Ondatra zibethicus om c c c c

deer mouse Peromyscus maniculatus rg u u u u

western harvest mouse Reithrodontomys 

megalotis

msg u u u u
Stone Lakes NWR Comprehensive Conservation Plan 223

Common Name Scientific Name Habitat Sp S F W

Family GEOMYIDAE (gophers)

Botta’s Pocket Gopher Thomomys bottae g u u u u

Family MURIDAE (Old World mice, rats)

house mouse Mus musculus sgru u u u u

Norway rat Rattus norvegicus sgru u u u u

black rat Rattus rattus sgru u u u u

Family SCIURIDAE (chipmunks, squirrels, marmots)

western gray squirrel Sciurus griseus sg u u u u

Fox Squirrel Sciurus niger rg u u u u

California ground squirrel Spermophilus beecheyi rg u u u u
224 Stone Lakes NWR Comprehensive Conservation Plan

Stone Lakes NWR Birds

Common Name Scientific Name Habitat Sp S F W

Order ANSERIFORMES (waterfowl) 

Family ANATIDAE (ducks, geese and swans)

wood duck* Aix sponsa osr c c c c

greater white-fronted goose Anser albifrons oga o - u c

northern pintail Anas acuta s u r c c

american wigeon Anas americana s c - c a

northern shoveler Anas clypeata s a r u a

green-winged teal Anas crecca s c - c c

cinnamon teal* Anas cyanoptera msg c o o c

blue-winged teal Anas discors s r - r r

eurasian wigeon Anas penelope s - - - r

mallard* Anas platyrhynchos msg a a a a

gadwall* Anas strepera msg c r r c

lesser scaup Aythya affinis os u - - u

redhead Aythya americana os r - - r

ring-necked duck Aythya collaris os o - - c

greater scaup Aythya marila os - - - #

canvasback Aythya valisineria os r - - c

bufflehead Bucephala albeola os o - - c

common goldeneye Bucephala clangula os - - - u

barrow’s goldeneye Bucephala islandica os - - - #

canada goose* Branta canadensis osg o o o o

snow goose Chen caerulescens osga - - - r

ross’ goose Chen rossii osga - - - r

tundra swan Cygnus buccinator osa - - - o

hooded merganser Lophodytes cucullatus os r - - o

common merganser Mergus merganser os r - - r

ruddy duck* Oxyura jamaicensis os o r r o

Order APODIFORMES (swifts and hummingbirds) 

Family APODIDAE (swifts) 

white-throated swift Aeronautes saxatalis a r r r r

Vaux’s swift Chaetura vauxi a r - r -

Family TROCHILIDAE (hummingbirds) 

black-chinned hummingbird* Archilochus alexandri r r r u -

Anna’s hummingbird* Calypte anna r c c c u

Rufous/Allen’s hummingbird Selasphorus rufus r - - r -

Order CHARADRIIFORMES (shorebirds) 

Family CHARADRIIDAE (plovers and lapwings)

semipalmated plover Charadrius semipalmatus s r - r -

killdeer* Charadrius vociferus wide a a a a
Stone Lakes NWR Comprehensive Conservation Plan 225

Common Name Scientific Name Habitat Sp S F W

black-bellied plover Pluvialis squatarola s o - u c

Family LARIDAE (gulls and terns) 

black tern Chlidonias niger osa # - - -

herring gull Larus argentatus osa o - - c

California gull Larus californicus osa o r c c

Mew Gull Larus canus osa # - r r

ring-billed gull Larus delawarensis osa o - c c

Thayer’s gull Larus glaucoides osa - - # -

Bonaparte’s gull Larus philadelphia osa - r r #

Caspian tern* Sterna caspia osa o r o -

Forster’s tern Sterna forsteri osa c r r o

Family RECURVIROSTRIDAE (avocets and stilts) 

black-necked stilt* Himantopus mexicanus s c o c c

american avocet* Recurvirostra americana s o u o o

Family SCOLOPACIDAE (sandpipers and phalaropes)

spotted sandpiper Actitis macularius s o r o o

ruddy turnstone Arenaria interpres s # - - -

sanderling Calidris alba s # - - -

dunlin Calidris alpina s c - a a

baird’s sandpiper Calidris bairdii s - - # -

western sandpiper Calidris mauri s c - c o

pectoral sandpiper Calidris melanotos s - - # -

least sandpiper Calidris minutilla s c o c a

semipalmated sandpiper Calidris pusilla s - - r -

willet Catoptrophorus 

semipalmatus 

s # - - -

common snipe Gallinago delicata s u r o c

short-billed dowitcher Limnodromus griseus s - # - -

long-billed dowitcher Limnodromus scolopaceus s c - c c

whimbrel Numenius phaeopus sga o - r -

long-billed curlew Numenius americanus sga o r o o

red-necked phalarope Phalaropus lobatus s r - r -

wilson’s phalarope* Phalaropus tricolor s o r r -

ruff Philomachus pugnax s # - - -

lesser yellowlegs Tringa flavipes s o - o o

greater yellowlegs Tringa melanoleuca s c r c c

solitary sandpiper Tringa solitaria s # - # -

Order CICONIIFORMES (storks, herons and relatives) 

Family ARDEIDAE (bitterns, herons and egrets) 

great blue heron* Ardea herodias wide a a a a

great egret* Ardea alba wide a a a a
226 Stone Lakes NWR Comprehensive Conservation Plan

Common Name Scientific Name Habitat Sp S F W

American bittern* Botaurus lentiginosus m o o o u

cattle egret Bubulcus ibis g - - r r

green heron* Butorides virescens mr o o o o

snowy egret* Egretta thula ms c u c c

least bittern Ixobrychus exilis m r r r -

black-crowned night-heron* Nycticorax nycticorax mr o o o o

Family CATHARTIDAE (vultures) 

turkey vulture* Cathartes aura a a a a a

Family THRESKIORNITHIDAE (ibises) 

white-faced ibis Eudocimus albus sg o o o -

Order COLUMBIFORMES (pigeons) 

Family COLUMBIDAE (doves and pigeons)

rock dove* Columba livia u c c c c

mourning dove* Zenaida macroura wide c c c c

Order CORACIIFORMES (kingfishers and relatives) 

Family ALCEDINIDAE (kingfishers) 

belted kingfisher* Ceryle alcyon ra c c c c

Order FALCONIFORMES (diurnal birds of prey) 

Family ACCIPITRIDAE (osprey, kites, eagles and hawks) 

osprey Pandion haliaetus ra r r r -

cooper’s hawk* Accipiter cooperii ra u u c c

sharp-shinned hawk Accipiter striatus ra o o o o

golden eagle Aquila chrysaetos sga o o o o

red-tailed hawk* Buteo jamaicensis wide a a a a

red-shouldered hawk* Buteo lineatus ra a a a a

rough-legged hawk Buteo lagopus mga - - - r

ferruginous hawk Buteo regalis sa - - - r

swainson’s hawk* Buteo swainsoni rsga o c u -

northern harrier* Circus cyaneus msga a c a a

white-tailed kite* Elanus leucurus wide c c c c

bald eagle Haliaeetus leucocephalus a - - - #

Family FALCONIDAE (falcons) 

merlin Falco columbarius rga r - - o

prairie falcon Falco mexicanus msga r - - r

peregrine falcon! Falco peregrinus msga r - r r

american kestrel* Falco sparverius wide a a a a

Order GALLIFORMES (megapodes, curassows, pheasants, quails and relatives)

Family PHASIANIDAE

ring-necked pheasant* Phasianus colchicus rg a a a a

Family ODONTOPHORIDAE 
Stone Lakes NWR Comprehensive Conservation Plan 227

Common Name Scientific Name Habitat Sp S F W

california quail* Callipepla californica rg c c c c

Order GRUIFORMES (coots, cranes and rails)

Family GRUIDAE (cranes) 

sandhill crane Grus canadensis sg r - c c

Family RALLIDAE 

American coot* Fulica americana ms c o o a

common moorhen* Gallinula chloropus m o o o o

sora* Porzana carolina m o o o o

Virginia rail* Rallus limicola m o o o o

Order PASSERIFORMES (perching birds)

Family AEGITHALIDAE (bushtits) 

bushtit* Psaltriparus minimus r a a a a

Family ALAUDIDAE (larks) 

horned lark Eremophila alpestris g o - c c

Family BOMBYCILLIDAE (waxwings) 

cedar waxwing Bombycilla cedrorum r u - u u

Family CARDINALIDAE (grosbeaks and buntings) 

lazuli bunting* Passerina amoena r u u - -

blue grosbeak* Passerina caerulea r u u - -

black-headed grosbeak* Pheucticus melanocephalus r c c - -

Family CERTHIIDAE (creepers) 

brown creeper Certhia americana r - - # #

Family CORVIDAE (jays, magpies and crows) 

western scrub-jay* Aphelocoma californica rs a a a a

American crow* Corvus brachyrhynchos rsg c c c c

yellow-billed magpie* Pica nuttalli rsg o o o o

Family EMBERIZIDAE (towhees and sparrows) 

spotted towhee* Pipilo maculatus r a a a a

dark-eyed junco Junco hyemalis r u - u c

swamp sparrow Melospiza georgiana g - - # -

Lincoln’s sparrow Melospiza lincolnii gs u - - o

song sparrow* Melospiza melodia mr c c c c

savannah sparrow Passerculus sandwichensis gs a - a a

fox sparrow Passerella iliaca r o - r o

California towhee* Pipilo crissalis r u u u u

vesper sparrow Pooecetes gramineus g # - - -

chipping sparrow Spizella passerina g # # - -

white-throated sparrow Zonotrichia albicollis gs r - - r

golden-crowned sparrow Zonotrichia atricapilla gs r - c a

white-crowned sparrow Zonotrichia leucophrys gs r - c a
228 Stone Lakes NWR Comprehensive Conservation Plan

Common Name Scientific Name Habitat Sp S F W

Family FRINGILLIDAE (finches) 

lesser goldfinch* Carduelis psaltria g - - r r

American goldfinch* Carduelis tristis g c c c c

house finch* Carpodacus mexicanus wide a a a a

pine siskin Carduelis pinus r - - r -

purple finch Carpodacus purpureus r - - - #

Family HIRUNDINIDAE (swallows) 

barn swallow* Hirundo rustica msra c c c -

cliff swallow* Petrochelidon pyrrhonota msra a a o -

northern rough-winged 

swallow* 

Stelgidopteryx serripennis msra u o r -

tree swallow* Tachycineta bicolor msra a a o r

violet-green swallow Tachycineta thalassina msra - - r -

Family ICTERIDAE (icterids) 

red-winged blackbird* Agelaius phoeniceus mg a a a a

tricolored blackbird Agelaius tricolor mg o o r r

Brewer’s blackbird* Euphagus cyanocephalus us a a a a

bullock’s oriole* Icterus bullockii r u u - -

hooded oriole Icterus cucullatus r r - - -

brown-headed cowbird* Molothrus ater wide c c c o

great-tailed grackle* Quiscalus mexicanus sg r r r r

western meadowlark* Sturnella neglecta g a a a a

yellow-headed blackbird Xanthocephalus 

xanthocephalus 

m r r - -

Family LANIIDAE (shrikes) 

northern shrike Lanius excubitor gr - - - #

loggerhead shrike* Lanius ludovicianus gr u u u u

Family MIMIDAE (mockingbirds and thrashers)

northern mockingbird* Mimus polyglottos rg o o o o

Family MOTACILLIDAE (wagtails and pipits) 

American pipit Anthus rubescens sg c - u c

Family PARIDAE (titmice) 

oak titmouse* Baeolophus inornatus r u u u u

Family PARULIDAE (warblers) 

yellow-rumped warbler Dendroica coronata r c - c a

black-throated gray warbler Dendroica nigrescens r o - u r

yellow warbler Dendroica petechia r c r c -

townsend’s warbler Dendroica townsendi r o - o -

common yellowthroat* Geothlypis trichas mr c c c u

yellow-breated chat Icteria virens r # - - -

Macgillivray’s warbler Oporornis tolmiei r o - u -
Stone Lakes NWR Comprehensive Conservation Plan 229

Common Name Scientific Name Habitat Sp S F W

northern waterthrush Seiurus noveboracensis m # - - -

orange-crowned warbler Vermivora celata r c r c r

Nashville warbler Vermivora ruficapilla r r - r -

Canada warbler Wilsonia canadensis r - # - -

Wilson’s warbler Wilsonia pusilla r c - c -

Family PASSERIDAE (Old World sparrows) 

house sparrow* Passer domesticus u c c c c

Family REGULIDAE (kinglets) 

ruby-crowned kinglet Regulus calendula r c - c a

golden-crowned kinglet Regulus satrapa r r - u u

Family SITTIDAE (nuthatches) 

white-breasted nuthatch* Sitta carolinensis r u u u u

Family STURNIDAE (starlings) 

european starling* Sturnus vulgaris rs a a a a

Family SYLVIIDAE (gnatchatchers) 

blue-gray gnatcatcher Polioptila caerulea r # - r -

Family THRAUPIDAE (tanagers) 

western tanager Piranga ludoviciana r u r u -

Family TIMALIIDAE (babbler) 

wrentit* Chamaea fasciata r c c c c

Family TROGLODYTIDAE (wrens) 

marsh wren* Cistothorus palustris m a a a a

rock wren Salpinctes obsoletus g # # # #

house wren* Troglodytes aedon r c c c u

bewick’s wren* Thryomanes bewickii mr u u u u

winter wren Troglodytes troglodytes r - - - r

Family TURDIDAE (thrushes)

hermit thrush Catharus guttatus r o - o o

Swainson’s thrush Catharus ustulatus r o - o -

varied thrush Ixoreus naevius r - - r r

mountain bluebird Sialia currucoides r - - - #

western bluebird Sialia mexicana rg # - - #

American robin* Turdus migratorius rg c u c c

Family TYRANNIDAE (flycatchers) 

olive-sided flycatcher Contopus cooperi r r - o -

western wood-pewee* Contopus sordidulus r r - o -

pacific-slope flycatcher Empidonax difficilis r r r r -

hammond’s flycatcher Empidonax hammondii r # - r -

dusky flycatcher Empidonax oberholseri r # # - -

willow flycatcher Empidonax traillii r r - o -

ash-throated flycatcher* Myiarchus cinerascens rg u c r -
230 Stone Lakes NWR Comprehensive Conservation Plan

Common Name Scientific Name Habitat Sp S F W

black phoebe* Sayornis nigricans mr a a a a

say’s phoebe Sayornis saya sg - - u u

tropical kingbird Tyrannus melancholicus rg - - - #

western kingbird* Tyrannus verticalis rg u c - -

Family VIREONIDAE (vireos) 

Cassin’s vireo Vireo cassinii r r - r -

warbling vireo Vireo gilvus r u - u -

Hutton’s vireo Vireo huttoni r r r r r

Order PELECANIFORMES (pelicans, tropicbirds, cormorants and relatives)

Family PELECANIDAE (pelicans)

American white pelican Pelecanus erythrorhynchos os c u o o

Family PHALACROCORACIDAE (cormorants) 

double-crested cormorant Phalacrocorax auritus o c c o c

Order PICIFORMES (woodpeckers and relatives) 

Family PICIDAE (woodpeckers) 

northern flicker* Colaptes auratus r c o c c

acorn woodpecker Melanerpes formicivorus r - - - #

Nuttall’s woodpecker* Picoides nuttallii r c c c c

downy woodpecker* Picoides pubescens r c c c c

red-breasted sapsucker Sphyrapicus nuchalis r - - r r

Order PODICIPEDIFORMES (grebes)

Family PODICIPEDIDAE (grebes)

clark’s grebe Aechmophorus clarkii o r r o o

western grebe Aechmophorus occidentalis o r r o o

horned grebe Podiceps auritus os r - r r

eared grebe Podiceps nigricollis oms r r r r

pied-billed grebe* Podilymbus podiceps oms c u a a

Order STRIGIFORMES (owls) 

Family TYTONIDAE (typical owls)

long-eared owl Asio otus srg - - - #

short-eared owl Asio flammeus msg - - - r

burrowing owl* Athene cunicularia f r r r r

great horned owl* Bubo virginianus r c c c c

western screech-owl Megascops kennicottii r r r r r

barn owl* Tyto alba wide c c c c

Habitats: o - Open water, lakes, creeks, ponds; m - Marshes, tule and cattail stands; s - seasonal wetlands, mudflats, 

flooded fields; r - Riparian forests; g - Grasslands; a - Aerial, usually observed in flight; wide - Widespread, found in 

a variety of habitats; u - urban 

Seasons: Sp - Spring, March through May; S - Summer, June through August; F - Fall, September through 

November; W - Winter, December through February 

Abundance: a - Abundant, expected to be observed 80 to 100 percent of the time in appropriate habitat; c - Common: 

60 to 80 percent; u - Uncommon: 30 to 60 percent; o - Occasionally: 10 to 30 percent; r - Rare: 0 to 10 percent; * 

- Birds known to nest locally; ! -Threatened/Endangered Species; # - Observed less than 10 times in the past 10 

years 
Stone Lakes NWR Comprehensive Conservation Plan 231 Appendix D. Fish Species Found on Stone Lakes NWR Common name (scientific name) North Stone Lake South Stone Lake SP Cut Meadowlark Lake Black- Crown Lake Nicolaus Pond Laguna Creek Morrison Creek Fishhead Lake Lost Lake Order ATHERINIFORMES (rainbow fishes and silversides) Family ATHERINIDAE (silversides) Inland Silverside (Menidia beryllina) x x x x x x x Order CLUPEIFORMES (anchovies and herrings) Family CLUPEIDAE (herrings, menhadens, pilchards, sardines, shads and sprats) American shad (Alosa sapidissima) x Threadfin shad (Dorosoma petenense) x x x x x x x x Order CYPRINIFORMES (suckers and minnows) Family CYPRINIDAE (carps and minnows) California roach (Hesperoleucus symmetricus) x x Carp (Cyprinus carpio) x x x x x x x x x Goldfish (Carassius auratus) x x x x x Golden shiner (Notemigonus crysoleucas) x x x Hardhead minnow (Mylopharodon conocephalus) x x x x x Sacramento blackfish (Orthodon microlepidotus) x x x x x x Sacramento pikeminnow (Ptychocheilus grandis) x x *Sacramento splittail (Pogonichthys macrolepidotus) Order CYPRINODONTIFORMES (killifishes) Family POECILIIDAE (livebearers and topminnows) Mosquitofish (Gambusia spp.) x x x x x x x Order PERCIFORMES (perch-likes) Family MORONIDAE (temperate basses) Striped Bass (Morone saxatilis) x Family CENTRARCHIDAE (sunfish and sunfishes) Black Crappie (Pomoxis nigromaculatus) x x x x x x x x x Bluegill (Lepomis macrochirus) x x x x x x x x Crappie (Pomoxis spp.) x x x x Green sunfish (Lepomis cyanellus) x
232 Stone Lakes NWR Comprehensive Conservation Plan Hybrid sunfish (Lepomis spp.)

x

Largemouth bass (Micropterus salmoides)

x

x

x

x

x

Redear sunfish (Lepomis microlophus)

x

x

x

Warmouth (Lepomis gulosus)

x

x

x

x

x

White Crappie (Pomoxis annularis)

x

x

x

x

x

x

x

x

Family PECIDAE (perches and true perches)Bigscale logperch (Percina macrolepida)

x

x

x

x

x

x

Order SCORPAENIFORMES (scorpion fishes and sculpins)

Family COTTIDAE (scaleless sculpins and sculpins) Prickly sculpin (Cottus asper)

x

Sculpin (Cottus spp.)

x

x

Order 

Siluriformes (catfishes)

Family ICTALURIDAE (bullhead catfishes and North American freshwater catfishes) Black bullhead (Ictalurus melas)

x

x

x

x

x

x

x

Brown bullhead (Ictalurus nebulosus)

x

x

x

x

x

Bullhead (Ictalurus ssp.)

x

x

x

x

x

Channel catfish (Ictalurus punctatus)

x

x

x

x

Yellow bullhead (Ameiurus natalis)

x

x

x

White catfish (Ictalurus catus)

x

x

x

x

x

* presumed to be intermitently present after flooding events allow entry to the Refuge.
Stone Lakes NWR Comprehensive Conservation Plan 233

Appendix E. Wilderness Review 

A wilderness review is the process used by the Service to determine whether or not to 

recommend lands or waters in the National Wildlife Refuge System to Congress for 

designation as wilderness. The Service is required to conduct a wilderness review for each 

refuge as part of the CCP process. Lands or waters that meet the minimum criteria for 

wilderness are identified in a CCP and further evaluated to determine whether they merit 

recommendation for inclusion in the Wilderness System. 

According to the Wilderness Act of 1964 (16 USC 1131-1136; 78 Stat. 890), “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.” 

Stone Lakes National Wildlife Refuge contains a total of 1,738.8 discontinuous acres 

owned in fee title, by the Service. In addition 2,617.9 acres are managed under cooperative 

agreements and 1,519.9 acres are under easements. The Refuge is adjacent to a residential 

subdivision and a major interstate highway. The largest contiguous portion of land in fee 

ownership is about 840 acres, which is smaller than the area required for designation as 

wilderness. Moreover, the Refuge contains much evidence of past and current human use, 

including roads, actively managed wetlands, and remnants of past and current ranching and 

farming activities. For these reasons, Stone Lakes National Wildlife Refuge does not meet 

the criteria for wilderness designation. 
234 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 235

Appendix F. Endangered Species Act, Section 7 Consultation
236 Stone Lakes NWR Comprehensive Conservation Plan

Health Unit have not recorded the Delta smelt within Refuge waterways. Due to the presence of the 

Lambert Road flood control structure, the Stone Lakes Basin has an unimpeded hydrologic connection 

with the rest of the Delta only during major flood events. For the Delta green ground beetle we have 

made this determination because the species has not been documented on the refuge and no suitable 

habitat for this species is present (Chris Nagano, pers. comm.). For the California red-legged frog 

we have made this determination because this species is believed to be extirpated in this area of the 

Sacramento Valley floor due to a number of factors. For the California tiger salamander, we have made 

this determination because surveys over the last ten years on the refuge have failed to document this 

species. In addition, the location of the refuge in the floodplain and the soil types present on the refuge 

are not compatible with the presence of this species.

The National Wildlife Refuge System Improvement Act of 1997 mandated that all National Wildlife 

Refuges (NWRs) prepare Comprehensive Conservation Plans (CCP). The purpose of this consultation 

is to determine potential effects of routine Refuge projects, activities, and programs on listed or 

proposed species, to authorize take incidental to those actions, and to expedite review of new 

acquisitions, restoration projects, programs, or management plans. The Refuge and the SFWO have 

determined that although management and restoration of habitats on the Refuge benefit listed species in 

the long term, some activities may adversely affect listed species and may result in incidental take, thus 

requiring consultation under the Act. Projects which exceed the scope of activities described in this 

biological opinion may require individual biological opinions. Significant projects will be reviewed on 

a case by case basis to determine the need for additional consultation.

Consultation History 

The SFWO has previously reviewed the Refuge Integrated Pest Management (IMP) Proposals for 

mosquito abatement and for water hyacinth control, as well as reviewed other proposed actions on the 

Refuge, and these consultations are incorporated by reference:

March 27, 1995: The SFWO concurred with the determination that the use of the bacterium

Bacillus thuringiensis israelensis (Bti) and Altocid® (methoprene) for mosquito control at the 

Stone Lakes NWR is not likely to adversely affect the vernal pool fairy shrimp, vernal pool 

tadpole shrimp, giant garter snake, valley elderberry longhorn beetle, Sacramento splittail, and 

delta smelt (SFWO file: 1-1-95-I-0680). 

NOTE: Although Altocid (methoprene) was authorized for use on the refuge in our March 27, 

1995, letter, research has shown that this pesticide can have deleterious effects on vernal pool 

crustaceans. The use of methoprene, a growth hormone, may result in the delay of development 

of adult vernal pool crustaceans which may reduce the number of resting eggs (cysts) that are 

formed before the pools dry (Lawrenz 1984). Because of the effects of methoprene on vernal 

pool crustaceans and a lack of information on how long the agent remains in the soil, we wish 

to clarify that methoprene will not be used within vernal pools or swales at any time, in either 

wet or dry conditions. A buffer of at least 300 feet would separate vernal pools and swales from 

areas where methoprene would be used. As of this date, methoprene has never been used at the 

Refuge.

May 25, 1995: The SFWO concurred with the determination that the use of Weedar 64® and 

Rodeo® to control water hyacinth was not likely to adversely affect the delta smelt, giant garter 

snake, and valley elderberry longhorn beetle, provided that mitigation measures identified in 

the letter were followed. These measures included: monitoring dissolved oxygen during water 

hyacinth die-off (for impacts to listed fish) and ceasing herbicide spray if the listed fish or giant 

garter snake were killed or harassed. For the valley elderberry longhorn beetle, if elderberry 

bushes were found in areas to be sprayed, the bushes would be flagged and avoided (SFWO file: 

1-1-95-I-0903). 

July 26, 1995: The SFWO issued a biological opinion which resulted in a conservation 
Stone Lakes NWR Comprehensive Conservation Plan 237

easement agreement to preserve and construct vernal pools as mitigation for the issuance of a 

404 Permit for the Elliot Ranch South Project (AKT parcel). (SFWO file number 1-1-99-F0118).

May 21 and June 10, 1996: The SFWO concurred that aerial spraying of the herbicide Rodeo 

for the control of water hyacinth was not likely to adversely affect the giant garter snake, 

valley elderberry longhorn beetle, delta smelt, or Sacramento splittail. To minimize drift of the 

herbicide, aerial applications were allowed only when wind speed was between 2 and 4 miles 

per hour. To prevent low dissolved oxygen levels caused by decomposing water hyacinth, no 

more than three contiguous acres would be treated at one time and 100 foot buffer strips would 

be left between treated sites. (SFWO files: FWS/EC96-040 and 1-1-96-I-640).

January 9, 1997: The SFWO concurred with the determination that the use of the bacterium 

Bacillus sphaericus for mosquito control, is not likely to adversely affect the vernal pool fairy 

shrimp, vernal pool tadpole shrimp, giant garter snake, valley elderberry longhorn beetle, delta 

smelt, or Sacramento splittail at the Stone Lakes NWR (SFWO file: 1-1-96-I-0639). 

July 26, 1999: The SFWO amended biological opinion 1-1-99-F-0118, to further refine 

required mitigation measures for the Elliot Ranch South Project (AKT parcel). 

More recently, the SWFO has reviewed the following routine Refuge operations:

January 31, 2001: The SFWO concurred that pest management activities at the Refuge are 

not likely to jeopardize the giant garter snake, valley elderberry longhorn beetle, vernal pool 

tadpole shrimp, or vernal pool fairy shrimp. (SFWO file:1-1-00-F-0162).

May 2, 2003: The SFWO concurred that the dredging of an existing channel that feeds water 

into permanent and seasonal wetlands on 457 acres would likely adversely affect, but would not 

jeopardize the giant garter snake. (SFWO file 1-1-03-F-0094).

July 16, 2003: The SFWO concurred that the mechanical shredding of water hyacinth was not 

likely to adversely affect the giant garter snake or the valley elderberry longhorn beetle. (SFWO 

file 1-1-03-I-2416).

January 3, 2005: The SFWO concurred that the Refuge waterfowl hunting program was 

not likely to adversely affect the giant garter snake, based on timing and monitoring efforts. 

(SFWO file 1-1-05-I-0323).

The Division of Endangered Species, Washington, D.C., consults annually on proposed Migratory 

Game Bird Hunting Regulations. The consultation addresses the effects to listed and proposed 

migratory birds of accidental shootings and potential lead poisoning through ingestion of lead shot. 

Listed migratory birds that occur on the Refuge that could be affected by Migratory Game Bird 

Hunting Regulations are the bald eagle. 

August 24, 2005, the Service concluded that Migratory Game Bird Hunting Regulations are 

not likely to adversely affect the bald eagle. Because incidental take of listed migratory birds 

has already been addressed in the Migratory Game Bird Hunting Regulations consultation, the 

SFWO will only address the effects, if any, of the Refuge hunt program to other listed species.

Management Plans:

The National Wildlife Refuge System Improvement Act of 1997 mandates the preparation of CCPs for 

all wildlife refuges within 15 years, which is the purpose of this consultation. 

Some projects or types of projects require more in-depth planning than the CCP process is designed 
238 Stone Lakes NWR Comprehensive Conservation Plan

to provide. For these projects, the Refuge prepares step-down management plans. In essence, stepdown management plans provide the additional planning details necessary to implement management 

strategies identified in a CCP. Refuge staff members have already completed a number of step-down 

plans. These include fire management, grazing, land protection, and the mosquito integrated pest 

management plans. The CCP proposes to include a volunteer and a comprehensive inventory and 

monitoring plan in the near future.

Programmatic Consultation Guidelines

This consultation covers the Refuges’ CCP which includes habitat restoration, routine management, 

maintenance, and operations activities carried out by the Refuge. These activities and programs 

are described in the project description below. Those activities outside the scope described, such as 

further changes in refuge management plans or new refuge programs may require further review. 

Upon request of the Refuge, the SFWO may agree to append additional projects or activities to this 

consultation.

Implementing Procedure

Projects and activities covered under this opinion are those activities that are described in the CCP and 

include the day-to-day management of the Refuge. Such activities also include habitat manipulation 

and restoration, modifications of existing structures, and repair and maintenance of levees, roads, 

trails, utilities, etc. Projects that may require further review may include restoration plans for new 

acquisitions to the Refuge, significant changes in land use on refuges, or new programs proposed for 

implementation on the Refuge. The SFWO expects that such projects, new activities, or new programs 

would require review and documentation pursuant to the National Environmental Policy Act (NEPA), 

and believes it would be appropriate to review those projects to ensure they meet the scope of this 

consultation. 

The following process will be used when reviewing additional proposed projects or programs for 

inclusion in this consultation:

1. The Refuge will submit a letter requesting that the proposed project be appended to this 

programmatic biological opinion and provide the SFWO with a biological assessment of the 

proposed action.

2. The SFWO will review the proposed project to determine: (1) the potential effects of the 

proposed project to listed species, (2) if it is appropriate to append the proposed project to this 

programmatic biological opinion, and/or (3) the proposed project should undergo a separate 

consultation.

3. Within 30 days, the SFWO will respond with an agreement to append the project to the 

programmatic consultation and/or with requests for information needed to complete a 

separate consultation. If additional consultation is necessary, the SFWO will initiate informal 

consultation upon receipt of a request from the Refuge and will contact the Refuge to request 

any additional information. Once the SWFO has received all the information necessary for 

consultation, we will initiate consultation.
Stone Lakes NWR Comprehensive Conservation Plan 239

BIOLOGICAL OPINION

Description of Management Area:

Introduction

Stone Lakes National Wildlife Refuge was established in 1994 becoming the 505th NWR. The refuge 

boundary encompasses 18,200 acres, including a core refuge of approximately 9,000 acres and a 9,000-

acre “Cooperative Wildlife Management Area”. Approximately 5,600 acres are currently managed 

by the Service. Stone Lakes NWR is located in the Sacramento Valley in the southwestern part of 

Sacramento County. The refuge lies about 10 miles south of Sacramento, straddling Interstate 5 from 

the town of Freeport south to Lost Slough.

Climate and Physiography

The Refuge lies between the Coast and Diablo Ranges to the west and the Sierra Nevada to the east. 

The Carquinez Strait provides a sea-level gap between the Coast Ranges and the Diablo Range. The 

Carquinez Strait is approximately 55 miles southwest of the refuge and the intervening terrain is mainly 

flat with rolling hills. Thus, this strait allows prevailing southerly winds from the coast to blow in. 

During winter, the sea breezes diminish and winds from the north occur more frequently. However, the 

winds from the south still predominate. Annual temperature in the area averages approximately 61.0 

F degrees and annual precipitation averages approximately 17.93 inches. Tule fog is common in the 

winter. 

Soils and Representative Vegetation

Seven general soil types are found within the Refuge: (1) Egbert clays and Valpac loams; (2) Gazwell 

mucky clays and Rindge muck and mucky loams; (3) Scribner clay loams, Sailboat and Cosumnes silt 

loams; (4) Columbia and Cosumnes sandy loams and silty loams; (5) Dierssen sandy clay loams and 

clay loams; (6) Clear Lake clays; and (7) San Joaquin sandy loams and silty loams.

The upland areas are dominated by introduced annual grasses interspersed with native perennial grasses 

and forbs. Valley oak savannah persists in well-drained alluvial soils which are not extensive within 

the refuge boundary. The understory typically supports annual grasses; however, moister soils support 

shrubs such as poison-oak and wild rose.

Riparian forests consist primarily of three types: (1) cottonwood riparian forests (2) mixed riparian 

forest, and (3) valley oak riparian forest. Cottonwood riparian forests occur along perennial streams 

where annual inundation occurs every spring, due to flooding. The forest canopy is dominated 

by Fremont cottonwood and Gooding’s willow, typically draped with California grapevine. The 

understory often supports California box elder, California blackberry, white-stemmed raspberry, 

buttonbush, and elderberry. Mixed riparian forests occur where inundation frequency and duration are 

intermediate between cottonwood and valley oak riparian forests. Canopy dominants include Fremont 

cottonwood, valley oak, Gooding’s willow, red willow, yellow willow, California black walnut, and 

California sycamore. Common understory dominants include California box elder, Oregon ash, poisonoak, and buttonbush. The California grape enveloping trees and shrubs often gives this forest a junglelike appearance. The upper portion of the floodplain has less frequent inundation and supports the 

valley oak riparian forest. The dense forest canopy is dominated by valley oak with associated tree 

species of Oregon ash, California sycamore, and California black walnut. Understory vines and shrubs 

include California blackberry, poison-oak, and wild rose.

Description of the Proposed Action

Biological Surveys/Collections

Bird surveys including ground surveys of waterbirds, mist netting, banding and marking landbirds, 

sandhill crane surveys, and colonial water bird rookery counts may be conducted. Annual vegetation 
240 Stone Lakes NWR Comprehensive Conservation Plan

monitoring, such as residual dry matter measurement, growing conditions, and surveys of vegetation 

type, is conducted in both managed wetlands and grasslands.

Scientific research on the Refuge is allowed on a case-by-case basis via a Special Use Permit (SUP). 

Historical research includes studies on the western pond turtle, yellow starthistle, sunflower parasitoids, 

and cattle grazing. Plant collections are allowed on the refuge for educational purposes (refuge 

herbarium), the California Indian Basketweavers Association, and for restoration and transplant 

purposes. Refuge staff is working on a proposal to do additional monitoring for the giant garter snake 

on the Refuge with the U.S. Geological Survey, Biological Resources Division.

Restoration Activities

Habitat restoration activities may include returning the land to its natural contours, installing water 

delivery and control structures, plantings, and removal or control of undesirable vegetation. Irrigation 

systems may be installed for riparian restoration. Native plant cultivation (native grasses, forbs, shrubs 

and trees) may be developed in refuge plant nurseries. Levee repair or levee and dike construction 

may be included in restoration activities. Wetland, riparian, and grassland restorations would be the 

most common type of restoration, although any suitable (Central Valley) natural plant community may 

be restored. Historical maps, aerial photographs, topography, hydrology, and soils will be assessed to 

determine the appropriate types of vegetation to be restored in a given area. Whenever possible, local 

plant strains (genotypes and phenotypes) will be used in restoration. A variety of heavy equipment 

(e.g., bottom scrapers, tractors, backhoes, etc.) could be used in the re-contouring of former agricultural 

lands, in the installation of pumps, pipelines, water control structures, and in the inundation of former 

agricultural land through pumping, weirs, and culverts.

Public Use

The Refuge will build and maintain facilities for hunting, fishing, wildlife observation, interpretation, 

education, and photography. Facilities will include hiking trails, parking areas, viewing platforms, 

boardwalks, boat-ramps, hunting and photo blinds, and interpretive structures. Boat-fishing and nonmotorized boating is also permitted. Hunting will be allowed at South Stone Lake only on Wednesdays 

and Saturdays, the remainder of the Refuge will be reserved as a sanctuary. 

Water Management Activities

Water management activities include managing the timing and duration of flood-up and drawdown for 

seasonal wetlands and summer irrigation to promote beneficial moist-soil vegetation. Water levels in 

permanent wetlands are maintained for resident wildlife and nesting bird species. Irrigation may occur 

to support riparian, grassland, and wetland restoration plantings. 

Routine Maintenance

Routine maintenance includes the repair of levees, roads, ditches, and waterways; vegetation 

management by mowing, disking, burning, spraying, or grazing; and the maintenance of waterways, 

easements and roads by clearing silt, trees, and shrubs. Heavy equipment (e.g., tractors, backhoes, 

excavators, etc.) use may be required for routine maintenance, repairs, enhancement, and restoration 

projects.

Prescribed Livestock Grazing

Prescribed grazing may be used to promote native plant communities in vernal pools, seasonal 

wetlands, and on lakeshores, and to discourage the growth of non-native grasses, noxious weeds and 

other undesirable vegetation. Grazing related activities include installing and maintaining fences, 

gates, corrals, windmills, troughs, and irrigation systems. Pasture inspections via horse and/or ATV by 

the permit holder will occur on a regular basis. Grassland production estimates and residual dry matter 

will be assessed annually by Refuge staff to monitor grassland condition.

Animal Damage Control

Live trapping and euthanasia of beaver and muskrat will be conducted in selected areas where damage 
Stone Lakes NWR Comprehensive Conservation Plan 241

to levees, roads, water control structures, and/or native plantings has occurred.

Special Use Permits

Research and other activities conducted by non-refuge personnel on the Refuge are governed by SUPs. 

SUPs are designed to allow appropriate activities while minimizing impacts to Refuge wildlife and 

habitats, with emphasis on avoidance of any sensitive areas or species. Research on listed species also 

requires a separate federal 10(a)(1)(A) recovery permit.

Herbicide/Pesticide Use

Invasive and noxious plant control efforts on the Refuge are a major part of habitat management. 

Current efforts include control and treatment of non-native aquatic and terrestrial vegetation such 

as water hyacinth, Egeria densa, and other submergents, perennial pepperweed, yellow starthistle, 

cocklebur, thistle species, giant cane, and others. Equipment used in the treatment of invasive plants 

includes boats, airboats, ATVs, truck-and-trailer, and handheld apparatus. Incidental take associated 

with these actions has been covered through the Section 7 process and this consultation and biological 

opinion is incorporated by reference. Various environmental data associated with this activity are 

collected for monitoring and management purposes (1-1-00-F-0162).

The Refuge is using the Weed Management Information System, developed by The Nature 

Conservancy. This information system is used to document the location of specific weed management 

treatments through the use of a Global Positioning System to determine the effectiveness of treatments.

All Refuge staff applying pesticides are required to have a California Qualified Applicator certificate. 

Refuge staff have received training in the identification of elderberry plants, the valley elderberry 

longhorn beetle, and the locations of vernal pools and giant garter snake habitat. Refuge staff have 

attended training held by the California Department of Boating and Waterways, which included 

training in the protocol to use if a giant garter snake is seen when applying herbicide.

Mosquito Abatement

The Refuge staff works closely with the Sacramento/Yolo Mosquito Vector Control District (SYMVCD 

) to reduce or eliminate mosquitoes on the Refuge. The Refuge entered into an MOU with SYMVCD 

in 1993. This MOU outlines an effective mosquito suppression program that includes biological 

and chemical controls to be used on the Refuge, wetland design and water level management 

recommendations, and research partnerships. The MOU is annually updated and renewed. Biological 

controls include the placement of mosquito fish and guppies in permanent and seasonal wetlands and 

the use of Bti, which is a very effective method for controlling mosquito larvae. All of the treatments 

over the past two years have been limited to biological control methods, although chemical controls 

are also an option if warranted. Chemicals to be used on the Refuge are approved by the Service prior 

to the mosquito season in early spring. These chemicals target larvae and adults and can include aerial 

applications, as well as ground application(s).

Fire Management

Prescribed burning of wetland and grassland habitats to remove excess vegetation, control non-native 

species, and maintain habitat value may occur. Brush pile burning and strip fires to reduce fuel load 

and the threat of wildfires and to reduce threats of fire along the urban interface may occur.

Goals of the Proposed Action

In addition to the management activities described above, the Refuge has identified a list of goals 

which are descriptive, open-ended, and often broad statements of desired future conditions that convey 

a purpose but do not define measurable units. Goals translate Refuge purposes into management 

direction. Each goal is supported by measurable, achievable objectives with specific strategies 

needed to accomplish them. These strategies are described in the CCP. Objectives are designed to 
242 Stone Lakes NWR Comprehensive Conservation Plan

be accomplished within 15 years. Actual implementation, however, may vary as a result of available 

funding. 

Goal 1. Conserve, enhance, restore, and manage Central Valley wetland, riparian, grassland, and 

other native habitats to benefit their associated fish, wildlife, plants, and special status species. 

Objective 1.A. Within 15 years, plant a minimum of 65 acres of valley foothill riparian and oak 

woodland habitat with a canopy cover of 20-80% and a canopy height of 2-10 meters. These newly 

planted habitats would have a complex structure with a canopy, subcanopy, and understory shrub layer 

that would continue to mature after the lifetime of this CCP. An additional 40 acres of understory 

shrubs and herbaceous cover would be established in areas restored from 1995-1998. These restored 

habitats would provide breeding and migratory habitat for a variety of riparian dependent species which 

have been identified by the Central Valley Joint Venture as species of concern including: (1) yellow 

warbler, (2) song sparrow, (3) spotted towhee, (4) yellow breasted chat, (5) black headed grosbeak, and 

(6) common yellowthroat..

Objective 1.B: Maintain and manage on an annual basis, 425 acres of riparian and oak woodland 

habitat, consisting of 360 acres of existing habitat and 65 acres of restored habitat. This habitat 

encompasses riparian and oak woodland habitat in various successional stages comprising a complex 

structure with a canopy, subcanopy, and understory shrub layer (usually impenetrable). Restoration 

would occur through habitat manipulations, including vegetation control of invasive species and 

restoration of the subcanopy and understory shrub layer. These habitats provide breeding and migratory 

habitat for the following focal species for the Central Valley, as defined by the Central Valley Joint 

Venture (CVJV) (1) yellow warbler, (2) song sparrow, (3) spotted towhee, (4) yellow breasted chat, (5) 

black headed grosbeak, and (6) common yellowthroat. Furthermore, these riparian areas support heron 

and egret rookeries that vary in size from 10 to 50 nests.

Objective 1.C: Within five years, enhance and annually maintain approximately 50 acres of seasonal 

and permanent wetlands without water control structures on the 70-acre LIC tract of the South Stone 

Lake Unit by promoting the growth of wetland species such as swamp timothy, smartweeds, water 

grass, and associated invertebrate animals. 

Objective 1.D.a: Manage on an annual basis, 529 acres as moist soil habitat, characterized by a plant 

composition of 50 percent or more moist soil, high-energy waterfowl plant foods (e.g. watergrass, 

swamp timothy, and smartweeds). Flood approximately 60 percent of the moist soil units to a depth of 

two to ten inches for dabbling ducks and shorebirds, and 40 percent to depths of six inches to three feet 

for diving ducks, grebes, pelicans, and other waterbirds.

Objective 1.D.b: Annually maintain 452 acres of seasonal wetlands with no water control structures, 

characterized by a plant composition of 50 percent or more of moist soil, high energy waterfowl plant 

foods interspersed with open water. Control undesirable vegetation such as cocklebur, pepperweed, and 

yellow starthistle, to benefit wintering and migratory waterfowl, as well as other wetland-dependent 

species. 

Objective 1.D.c: Annually maintain 136 acres of vernal pool seasonal wetlands characterized by >70 

percent native vernal pool vegetation. 

Objective 1.E: Annually maintain 715 acres of deep-water wetlands (includes wetlands with and 

without water control capabilities), lakes, sloughs, and waterways, to provide breeding, foraging, and 

loafing habitat for waterfowl and other wetland dependent species, such as giant garter snakes and 

western pond turtles. Deep water wetlands are characterized by water depths of >3 feet with wetland 

plants species such as tules, cattails, burreed, and water primrose. 

Objective 1.F: Manage and enhance approximately 1,900 acres of dry (non-irrigated) grasslands on 
Stone Lakes NWR Comprehensive Conservation Plan 243

the North Stone Lake Unit on an annual basis, to provide a variety of grass heights and densities as 

measured by residual dry matter (RDM) at the end of the grazing season (Aug-Sept). The rotation of 

grazing pressure in the different pasture units will support a diversity of grassland dependent species 

including sandhill cranes, arctic nesting geese, raptors, shorebirds, and songbirds including the 

following species identified by the USFWS as species of conservation concern: sandhill crane, longbilled curlew.

Objective 1.G: Annually maintain 460 acres of irrigated pasture/wet meadow to provide habitat for a 

variety of grassland dependent species including sandhill crane, white faced ibis, long-billed curlew, 

and arctic nesting geese.

Objective 1.H: Restore approximately 30 acres to grassland habitat consisting of a minimum of 70 

percent native grasses (Stipa pulchra, Poa spp., Leymus spp., Elymus spp., and Mellica spp.) on various 

Refuge units within ten years to promote biodiversity and improve the grassland communities on the 

Refuge.

Objective 1.I: Within 15 years, coordinate Refuge land conservation program to protect 75 percent of 

the land within the approved Refuge boundary to help achieve the CVJV regional habitat protection 

goals.

Objective 1.J: Coordinate Refuge habitat conservation with other private and public conservation 

efforts within the Sacramento-San Joaquin Delta to contribute to regional habitat conservation needs.

Objective 1.J.a: Manage Refuge floodplain lands in a manner consistent with local, State, and Federal 

flood management, sediment and erosion control, and water quality objectives as

described in the Environmental Impact Statement associated with Refuge establishment.

Objective 1.J.b: Within 10 years of CCP approval, work toward achieving the water quality supply 

standard set forth by the U.S. Environmental Protection Agency, California Department of Fish and 

Game, and the Regional Water Quality Control Board, for wetlands and fish and wildlife resources.

Goal 2. Conserve, enhance, and restore high quality migrating, wintering, and breeding habitat 

for migratory birds within the Sacramento-San Joaquin Delta of the Central Valley.

Objective 2.A: Manage 2,950 acres of Refuge lands and work with adjacent landowners to protect 

agricultural lands and habitats that support a wintering population of 200-300 greater sandhill cranes 

and 200 lesser sandhill cranes from September through March. Shallow water will be maintained in 

irrigated pastures to provide roosting and foraging habitat; dry pastures, wheat, corn, and alfalfa fields 

will be sowed to provide foraging habitat.

Objective 2.B: Develop monitoring strategies for focal species identified in various regional bird 

conservation plans, to assess current and guide future habitat restoration activities. The regional 

plans include the following: Central Valley Joint Venture Plan, Riparian Bird Conservation Plan, 

Grassland Bird Conservation Plan, Oak Woodland Bird Conservation Plan, North American Waterbird 

Conservation Plan, North American Waterfowl Management Plan, and North American Landbird 

Conservation Plan. The Service’s Birds of Conservation Concern are addressed within these various 

plans.

Goal 3. Provide visitors with wildlife-dependent recreation, interpretation, and educational 

opportunities which foster an understanding of the Refuge’s unique wildlife and plant 

communities in an urban setting. 

Objective 3.A: Recruit and maintain sufficient short and long term volunteers to accomplish habitat 
244 Stone Lakes NWR Comprehensive Conservation Plan

restoration projects, wildlife surveys, and environmental education programs.

Objective 3.B: Construct adequate facilities and develop programs for the public to visit the Refuge 

seven days a week.

Objective 3.C: Within five years, develop an environmental education program with a target of 

providing 80 groups per year with an outdoor experience where visitors become aware of the Refuge’s 

role in the conservation of Central Valley and Sacramento-San Joaquin Delta habitats and their fish and 

wildlife.

Objective 3.D: Within five years, develop two interpretive programs where visitors can learn of the 

Refuges’ role in conserving the Central Valley and Sacramento-San Joaquin Delta habitats and their fish 

and wildlife with an emphasis on outdoor hands-on experiences.

Objective 3.E: Within five years, the Refuge will provide safe boat-only fishing with day-use parking 

facilities for approximately 20 boats on South Stone Lake, and approximately 10 boats on SP Cut from 

June through September. 

Objective 3.F: Continue and expand the Refuge outreach program, targeting the local community 

and nontraditional users, by expanding partnerships for the annual “Walk on the Wildside” event. 

Participate in a minimum of four appropriate off-Refuge events to increase awareness of the Refuges’ 

role in the conserving Central Valley and Sacramento-San Joaquin Delta habitats and their associated 

fish and wildlife.

Conservation Measures

Giant garter snakes

The Refuge will adhere to all guidelines listed in the Service’s November 1997, Standard Avoidance 

and Minimization Measures During Construction Activities in Giant Garter Snake (Thamnophis gigas) 

Habitat and Guidelines for Restoration and/or Replacement of Giant Garter Snake Habitat.

Avoidance measures for earth moving activities:

1. Earth moving activities will be restricted to May through October, during the 

majority of the giant garter snakes’ active period when snakes are able to escape 

and avoid danger. During the giant garter snakes’ inactive period (November 1 

through April 1) some small-scale emergency levee repair may occur, but will 

usually be less than 20 linear feet.

2. All earth moving activities will occur within wetlands that have been drained. 

Because these drained wetlands will not provide foraging habitat, it is likely 

that giant garter snakes will not remain for extended periods after they are 

drained. This reduces the chance that any earth moving activities will harm or 

harass snakes. Drained areas will be dry for at least two weeks prior to earth 

moving activities. Drained areas also will be checked for ponded areas that may 

concentrate prey and become an attractant to giant garter snakes. Ponded areas 

will be avoided and surveyed for giant garter snakes before any activity occurs 

within them.

Avoidance measures for canal excavation/maintenance activities (including water control 

structure replacement):
Stone Lakes NWR Comprehensive Conservation Plan 245

1. Canal excavation will be performed only from May 1 to November 1.

2. Excavation will typically occur from only one side of the canal during a given 

year. When possible, one side of the canal will be left undisturbed indefinitely.

3. Excavation above the high flow watermark will be avoided whenever possible to 

minimize disturbance to burrows and retreat sites.

4. Vegetation on the tops and sides of canals will be left as undisturbed as possible.

Avoidance measures for vegetation management:

1. Roads adjacent to giant garter snake habitat will: a) not be mowed unless 

necessary for regular access; b) be mowed between March 1 and October 31; 

c) be mowed with mowers adjusted to leave no less than six inches of standing 

vegetation. These measures decrease the risk of injuring snakes and minimize 

loss and disturbance of vegetative cover.

2. Burning will be conducted during the spring, summer, and fall months on 

thoroughly dried wetlands or uplands. Where possible only one bank of 

vegetation will be subject to prescribed burns. Vegetation along canal banks 

will be left undisturbed as much as possible and fire crews will not reignite bank 

vegetation passed over by fire. Surveys for giant garter snakes will be conducted 

prior to burning, and any giant garter snakes observed within prescribed burn 

areas will be captured and relocated or attempts will be made to flush them away 

from areas where fire is likely to travel.

3. Disking will only take place during the giant garter snake active period. Disking 

will be conducted in dried wetlands or in uplands. Disking activities will be 

avoided directly adjacent to waterways and summer wetlands unless they have 

been allowed to dry. A 200 foot buffer between disking and wetlands or open 

water will be adhered to.

Habitat restoration and enhancement – The Refuge pursues fee title acquisition and cooperative 

management agreements for lands within or adjacent to existing refuge boundaries. Many restoration 

and enhancement projects have the potential to restore summer wetlands which provide giant garter 

snake habitat. The Refuge evaluates restoration projects to determine whether incorporation of 

essential habitat components for the giant garter snake is appropriate and feasible. Restoration 

activities generally require the same earth moving activities required for maintenance activities and 

would use the same conservation measures practiced for routine maintenance.

Maintenance and management changes – The Refuge is using several new techniques and materials to 

reduce the frequency of maintenance activities in wetlands and waterways. Over the next five years, 

the Refuge will replace corrugated metal water control structures with polyethylene and concrete 

structures. The new water control structures have a longer life expectancy (>30 years versus <10 years) 

and require less maintenance. Use of these structures will minimize the frequency of disturbance and 

risk of injury to giant garter snakes. In addition, rip-rap will be used to armor many of the structures, 

providing additional giant garter snake habitat and further minimizing maintenance needs. 

Valley elderberry longhorn beetle

The Refuge will adhere to all guidelines listed in the Service’s July 1999, Conservation Guidelines for 

the Valley Elderberry Longhorn Beetle. 
246 Stone Lakes NWR Comprehensive Conservation Plan

The Refuge avoids disturbance to elderberry shrubs whenever possible, trains field crews in elderberry 

plant identification, and follows the July 1999, Conservation Guidelines for the Valley Elderberry 

Longhorn Beetle developed by the SFWO. When trimming elderberry shrubs that interfere with road 

and utility easements, trimming activities will be limited, whenever possible, to the dormant period for 

the beetle, November through mid February. The Refuge also actively plants elderberry plants as part 

of their riparian restoration activities. 

Vernal pool species

Habitat management activities in vernal pool areas are limited to prescribed fire and grazing. The 

Refuge avoids intentionally flooding these areas and avoids/restricts equipment or vehicle traffic in 

these areas. Vernal pool fairy shrimp and vernal pool tadpole shrimp may be harmed, harassed, injured, 

or killed during surveys, monitoring, and management activities of vernal pool habitat. However, adherence to the April 1996, Interim Survey Guidelines to Permittees for Recovery Permits Under 

Section 10(a)(1)(A) of the Endangered Species Act for the Listed Vernal Pool Brachiopods will 

minimize the effects of surveys and monitoring activities on vernal pool crustaceans.

During prescribed burns, the following measures will be implemented: 1) vehicle traffic will not 

occur in vernal pool basins or within 20 feet of vernal pool basin perimeters; 2) only foot traffic and 

wheeled vehicles will be permitted in alkali meadow and vernal pool terrain; tracked equipment such 

as bulldozers will not be used in these areas; 3) firebreaks will not be disked or bladed in vernal pools. 

Fire breaks will be constructed in managed seasonal marshes bordering vernal pool areas, or at the edge 

of vernal pool areas (next to buildings, parking lots, levees, roads, or canals); 4) where possible, preexisting or natural firebreaks will be used; and 5) wet lines and/or biodegradable foam will be used to 

create firebreaks where edge or natural features are absent.

Mosquito Control

Generally, naturally-functioning seasonal swales and vernal pools are not considered significant 

mosquito producing areas and should not require any chemical treatments. Furthermore, seasonal 

wetlands are usually dry by the onset of the primary mosquito production season (June 1). In the 

event mosquito control is necessary in any seasonal wetland, Bti would be used. The edge of manmade impoundments will be mowed and disked to discourage mosquito production. Mosquito fish are 

routinely introduced on the Lewis Property.

Mosquito control will follow an ordered succession, using nonchemical treatments first (i.e., water 

control strategies, Bti, etc.), resorting to chemical treatment only when necessary, as determined 

through standard mosquito monitoring procedures. Whenever possible, mosquito production areas will 

be treated with non-chemical treatments before larvacides or adulticides are applied. Wetlands that 

have produced large mosquito populations in the past will be flooded as quickly as possible to minimize 

multiple emergences that may cause a need for the use of adulticides. Bti will be used where it can be 

applied effectively. Dimilin (larvicide) would only be applied directly to water in actively-managed 

seasonal impoundments on the Lewis Property or the Beach Lake Mitigation Bank, not to vernal pool 

areas. The Sacramento-Yolo Mosquito and Vector Control District does not consider vernal pools to 

be mosquito production habitat because natural wetlands usually have enough natural predators (e.g., 

dragonfly larvae) to control mosquitoes without the use of larvicides.

If chemical treatments are necessary, adulticides will be used as a last resort after all larvicide options 

have been considered. The adulticide Trumpet EC will be applied by ultra-low volume (U.L.V.) coldfoggers from ground vehicles. To minimize pesticide drift when using adulticides and larvicides, 

dispersing vehicles will follow routes on existing roads set up to fog downwind or outside buffers of 
Stone Lakes NWR Comprehensive Conservation Plan 247

91 meters (300 feet) from areas supporting listed or proposed special status species (vernal pool-alkali 

wetland habitats). All chemical applications will occur when wind speeds are between 2 and 8 mph. 

Specific information regarding application data for individual agents is provided in the current PUPs.

Habitat restoration programs

The Refuge participates in and implements the Central Valley Joint Venture Implementation Plan of the 

North American Waterfowl Management Plan; components of the Central Valley Project Improvement 

Act (CVPIA); and the Federal Native Plant Conservation Memorandum of Understanding. The Refuge 

participates in development and implementation of recovery plans for listed species.

Status of the Species/Environmental Baseline

Giant Garter Snake

The Service published a proposal to list the giant garter snake as an endangered species on December 

27, 1991 (56 FR 67046). The Service reevaluated the status of the snake before adopting the final rule. 

The snake was listed as a threatened species on October 20, 1993 (58 FR 54053). A draft giant garter 

snake recover plan was published in 1999 (Service 1999).

The giant garter snake is one of the largest garter snake species, reaching a total length of 

approximately 64 inches (162 centimeters). Females tend to be slightly longer and proportionately 

heavier than males. The weight of adult female snakes is typically 1.1-1.5 pounds (500-700 grams). 

Dorsal background coloration varies from brown to olive with a cream, yellow, or orange dorsal 

stripe and two light colored lateral stripes. Some individuals have a checkered pattern of black spots 

between the dorsal and lateral stripes. Background coloration and prominence of the checkered pattern 

and three yellow stripes are geographically and individually variable; individuals in the northern 

Sacramento Valley tend to be darker with more pronounced mid-dorsal and lateral stripes (Hansen 

1980; Rossman et al. 1996). Ventral coloration is variable from cream to orange to olive-brown to pale 

blue with or without ventral markings (Hansen 1980). 

Giant garter snakes formerly occurred throughout the wetlands that were extensive and widely 

distributed in the Sacramento and San Joaquin Valley floors of California (Fitch 1940; Hansen and 

Brode 1980; Rossman and Stewart 1987). The historical range of the snake is thought to have 

extended from the vicinity of Chico, Butte County, southward to Buena Vista Lake, near Bakersfield, 

in Kern County (Fitch 1940; Fox 1948; Hansen and Brode 1980; Rossman and Stewart 1987). Early 

collecting localities of the giant garter snake coincide with the distribution of large flood basins, 

particularly riparian marsh or slough habitats and associated tributary streams (Hansen and Brode 

1980).

Loss of habitat due to agricultural activities and flood control have extirpated the snake from the 

southern one third of its range in former wetlands associated with the historic Buena Vista, Tulare, and 

Kern lake beds (Hansen 1980; Hansen and Brode 1980). By 1971, so much wetland habitat had been 

reclaimed, that the California Department of Fish and Game (CDFG) classified the giant garter snake 

as a rare animal and conducted a series of field surveys. The results of these surveys indicate that snake 

populations were distributed in marsh wetlands, tributary streams, and portions of the rice productions 

zones of the Sacramento Valley in Butte, Glenn, Colusa, Sutter, Yolo, and Sacramento Counties; 

in the Delta region along the eastern fringes of the Sacramento-San Joaquin River Delta in Solano, 

Contra Costa, Sacramento, and San Joaquin Counties; and in the San Joaquin Valley in San Joaquin, 

Stanislaus, Merced, Mendota, and Fresno Counties (Hansen 1988; Hansen and Brode 1980).

Upon federal listing in 1993, the Service identified 13 separate populations of giant garter snakes, with 

each population representing a cluster of discrete locality records (Service 1993). The 13 populations 
248 Stone Lakes NWR Comprehensive Conservation Plan

largely coincide with historical flood basins and tributary streams throughout the Central Valley: (1) 

Butte Basin, (2) Colusa Basin, (3) Sutter Basin, (4) American Basin, (5) Yolo Basin/Willow Slough, (6) 

Yolo Basin/Liberty Farms, (7) Sacramento Basin, (8) Badger Creek/Willow Creek, (9) Caldoni Marsh/

White Slough, (10) East Stockton--Diverting Canal & Duck Creek, (11) North and South Grasslands, 

(12) Mendota, and (13) Burrel/Lanare.

A population is a group of organisms that interbreed and share a gene pool. The boundaries of a 

population, both in space and time, are generally not discrete and, in practice, as usually defined 

by the researcher (Krebbs 1994). The gene pool and breeding patterns of the 13 giant garter snake 

populations identified in the final rule remain unstudied and unknown. What was described as “13 

populations” should therefore be described more accurately as sub-populations and occurrences that 

note observations of individuals about which much remains unknown (Service 1999).

Surveys over the last 25 years suggest that sub-populations of giant garter snake in the northern parts 

of its range (i.e., Butte, Colusa, and Sutter Counties) are relatively large and stable (Wylie et al. 1997; 

Wylie et al. 2003a, 2004a). Habitat corridors connecting sub-populations, however, are either not 

present or not protected, and urban encroachment increases as a serious threat (Service 1999). Subpopulations in Yolo, Sacramento, Solano, and San Joaquin Counties areas are small, fragmented, 

and threatened by urbanization (Hansen 2004; Service 1999). Those sub-populations in the San 

Joaquin Valley, however, are most vulnerable having suffered near-devastating declines and possible 

extirpations over the last two decades (including populations in Stanislaus, Merced, Madera and 

Fresno Counties) (Dickert 2002, 2003; Hansen 1988; Williams and Wunderlich 2003). The southern 

sub-populations are extremely small, distributed discontinuously in isolated patches, and therefore 

are highly vulnerable to extinction by random environmental, demographic, and genetic processes 

(Goodman 1987a).

Endemic to wetlands in the Sacramento and San Joaquin valleys, the giant garter snake inhabits 

marshes, sloughs, ponds, small lakes, low gradient streams, and other waterways and agricultural 

wetlands, such as irrigation and drainage canals, rice fields and the adjacent uplands (Service 1999). 

The snake feeds on small fishes, tadpoles, and frogs (Fitch 1941; Hansen 1988; Hansen and Brode 

1980, 1993). Essential habitat components consist of: (1) wetlands with adequate water during 

the snake’s active season (early-spring through mid-fall) to provide food and cover; (2) emergent, 

herbaceous wetland vegetation, such as cattails and bulrushes, for escape cover and foraging habitat 

during the active season; (3) upland habitat with grassy banks and openings in waterside vegetation 

for basking; and (4) higher elevation uplands for over-wintering habitat with escape cover (vegetation, 

burrows) and underground refugia (crevices and small mammal burrows) (Hansen 1988). Snakes are 

typically absent from larger rivers and other bodies of water that support introduced populations of 

large, predatory fish, and from wetlands with sand, gravel, or rock substrates (Hansen 1988; Hansen 

and Brode 1980; Rossman and Stewart 1987). Riparian woodlands do not provide suitable habitat 

because of excessive shade, lack of basking sites, and absence of prey populations (Hansen 1988). 

Giant garter snakes are the most aquatic garter snake species and are active foragers, feeding primarily 

on aquatic prey such as fish and amphibians (Fitch 1941). Historically, giant garter snake prey likely 

consisted of Sacramento blackfish (Orthodon microlepidots), thick-tailed chub (Gila crassicauda), and 

red-legged frog (Rana aurora) (Rossman et al. 1996; Service 1999). Because these prey species are no 

longer available (chub extinct, red-legged frog extirpated from the Central Valley, blackfish declining) 

the predominant food items are now introduced species such as carp (Cyprinus carpio), mosquitofish (Gambusia affinis), larval and sub-adult bullfrogs (Rana catesbiana), and Pacific chorus frogs 

(Pseudacris regilla) (Fitch 1941; Hansen and Brode 1993; Rossman et al. 1996).

The giant garter snake breeding season extends through March and April, and females give birth to 

live young from late July through early September (Hansen and Hansen 1990). Brood size is variable, 

ranging from 10 to 46 individual young, with a mean of 23 individuals (Hansen and Hansen 1990). 

At birth, young average about 8.1 inches (20.6 centimeters) snout-to-vent length and 3 to 5 grams. 
Stone Lakes NWR Comprehensive Conservation Plan 249

Although growth rates are variable, young typically more than double in size by one year of age, and 

sexual maturity averages three years in males and five years for females (Service 1993).

The giant garter snake is highly aquatic but also occupies a terrestrial niche (Service 1999; Wylie et al. 

2004a). Aquatic habitat includes remnant native marshes and sloughs, restored wetlands, low gradient 

streams, and agricultural wetlands including rice fields and irrigation and drainage canals. Terrestrial 

habitat includes adjacent uplands which provide areas for basking, retreats, and over-wintering. 

Basking takes place in tules, cattails, saltbush, and shrubs over-hanging the water, patches of floating 

vegetation including waterweed, on rice checks, and on grassy banks (Service 1999). The snake 

typically inhabits small mammal burrows and other soil and/or rock crevices during the colder months 

of winter (i.e., October to April) (Hansen and Brode 1993; Wylie et al. 1996; Wylie et al. 2003a). It 

also uses burrows as refuge from extreme heat during its active period (Wylie et al. 1997; Wylie et 

al. 2004a). While individuals usually remain in close proximity to wetland habitats, the Biological 

Resource Division of the U.S. Geological Survey (BRD) has documented snakes using burrows as 

much as 165 feet (50 meters) away from the marsh edge to escape extreme heat, and as far as 820 feet 

(250 meters) from the edge of marsh habitat for over-wintering habitat (Wylie et al. 1997). Snakes 

typically select burrows with sunny exposures along south and west facing slopes (Service 1993). In 

studies of marked snakes in the Natomas Basin, snakes moved about 0.25 to 0.5 miles (0.4 to 0.8 

kilometers) per day (Hansen and Brode 1993). Home range (area of daily activity) averages about 0.1 

mile2 (25 hectares) in both the Natomas Basin and the Colusa National Wildlife Refuge (NWR) (Wylie 

1998a; Wylie et al. 2002). Total activity, however, varies widely between individuals; individual 

snakes have been documented to move up to five miles (8 kilometers) over a few days in response 

to dewatering of habitat (Wylie et al. 1997) and to use up to eight miles (12.9 kilometers) of linear 

aquatic habitat over the course of a few months, and to have a home range as large as 14.5 miles2 (3744 

hectares) (Wylie and Martin 2004).

In agricultural areas, snakes were documented using rice fields in 19-20 percent of the observations, 

marsh habitat in 20-23 percent of observations, and canal and agricultural waterway habitats in 50-

56 percent of the observations (Wylie 1998b). In the Natomas Basin, habitat used consisted almost 

entirely of irrigation ditches and established rice fields (Wylie 1998a; Wylie et al. 2004b). In the 

Colusa NWR, snakes were regularly found on or near edges of wetlands and ditches with vegetative 

cover (Wylie et al. 2003a). Telemetry studies also indicate that active snakes use uplands extensively; 

more than 31 percent of observations were in uplands (Wylie 1998b). Snakes observed in uplands 

during the active season were consistently near vegetative cover, particularly where cover exceeded 50 

percent in the area within 1.6 feet (0.5 meter) of the snake (Wylie 1998b).

 

Snakes will move into restored habitat after two years. At the Colusa NWR, after two years, 

restoration area population estimates increased from 30 snakes per kilometer to 59-95 snakes per 

kilometer (Wylie et al. 2004a). At the Colusa Basin Drainage Canal, snakes were given three upland 

restoration treatments, 1) soil planted with native grasses over rock riprap, 2) soil planted with native 

grasses without rock, and 3) rock riprap only; snakes were most commonly found at the soil over rock 

riprap treatment (Wylie and Martin 2004). 

Giant garter snakes are eaten by a variety of predators, including raccoons (Procyon lotor), striped 

skunks (Mephitis mephitis), opossums (Didelphis virginiansa), bull frogs (Rana catesbiana), hawks 

(Buteo sp.), egrets (Casmerodius albus, Egretta thula), and great blue herons (Ardea herodias) (Dickert 

2003; Service 1999; Wylie et al. 2003c). Many areas supporting snakes have been documented to 

have abundant predators; however, predation does not seem to be a limiting factor in areas that provide 

abundant cover, high concentrations of prey items, and connectivity to a permanent water source 

(Hansen and Brode 1993; Wylie et al. 1996).

The current distribution and abundance of the giant garter snake is much reduced from former times 

(Service 1999). Less than ten percent, or approximately 319,000 acres (129,000 hectares), of the 

historic 4.5 million acres (1.8 million hectares) of Central Valley wetlands remain (U.S. Department of 
250 Stone Lakes NWR Comprehensive Conservation Plan

Interior 1994), of which very little provides habitat suitable for the giant garter snake. Loss of habitat 

due to agricultural activities and flood control have extirpated the snake from the southern one-third 

of its range in former wetlands associated with the historic Buena Vista, Tulare, and Kern lakebeds 

(Hansen 1980; Hansen and Brode 1980). These lakebeds once supported vast expanses of ideal snake 

habitat, consisting of cattail and bulrush dominated marshes (Service 1999). Cattail and bulrush 

floodplain habitat also historically typified much of the Sacramento Valley (Hinds 1952). Prior to 

reclamation activities beginning in the mid- to late-1800s, about 60 percent of the Sacramento Valley 

was subject to seasonal overflow flooding providing expansive areas of snake habitat (Hinds 1952). 

Valley flood wetlands are now subject to cumulative effects of upstream watershed modifications, 

water storage and diversion projects, as well as urban and agricultural development.

The Central Valley Project (CVP), planned by the State of California, and built and operated by the 

Federal Bureau of Reclamation, is the largest water management system in California. CVP and 

the historic water development activities that preceded it have not only resulted in the loss of all but 

approximately ten percent of wetlands, they have created an ecosystem altered to such an extent that 

remaining wetlands, like agriculture, depend on managed water (U.S. Department of Interior 1994). 

The historic disturbance events associated with seasonal inundation that occur naturally in dynamic 

riverine, riparian, and wetland ecosystems have been largely eliminated. In addition to the highly 

managed water regimes, implementation of the CVP has resulted in conversion of native habitats to 

agriculture, and has facilitated urban development through the Central Valley (Service 1999). In 1992, 

Congress enacted the CVPIA, the concerns of which include pricing and management of Central Valley 

water and attempting to mitigate for project impacts on fish, wildlife, and associated habitat. CVPIA, 

however, has been largely ineffective thus far, addressing primarily only the water needs of publiclyowned wetlands, which account for less than one-fourth of the wetlands in the Central Valley (Service 

1999).

Residential and commercial growth with the Central Valley is consuming an estimated 15,000 acres of 

Central Valley farmland each year (American Farmland Trust 1999). In the future, this transformation 

is expected to accelerate. Rice fields have become important habitat for giant garter snakes, 

particularly associated canals and their banks for both spring and summer active behavior and winter 

hibernation (Hansen 2004). While within the rice fields, snakes forage in the shallow water for prey, 

utilizing rice plants and vegetated berms dividing rice checks for shelter and basking sites (Hansen and 

Brode 1993). The loss of rice land resulting from residential and commercial growth compounds the 

impact of direct habitat loss resulting from development itself.

Ongoing maintenance of aquatic habitats for flood control and agricultural purposes eliminates 

or prevents the establishment of habitat characteristics required by snakes (Hansen 1988). Such 

practices can fragment and isolate available habitat, prevent dispersal of snakes among habitat units, 

and adversely affect the availability of the snake’s food items (Hansen 1988; Brode and Hansen 

1992). For example, tilling, grading, harvesting and mowing may kill or injure giant garter snakes 

(Service 1999; Wylie et al. 1997). Biocides applied to control aquatic vegetation reduce cover for the 

snake and may harm prey species (Wylie et al. 1996). Rodent control threatens the snake’s upland 

estivation habitat (Wylie et al. 1996; Wylie et al. 2004a). Restriction of suitable habitat to water canals 

bordered by roadways and levee tops renders snakes vulnerable to vehicular mortality (Wylie et al. 

1997). Materials used in construction projects (e.g., erosion control netting) can entangle and kill 

snakes (Stuart et al. 2001). Livestock grazing along the edges of water sources degrades water quality 

and can contribute to the elimination and reduction of available quality snake habitat (Hansen 1988). 

Fluctuation in rice and agricultural production affects stability and availability of habitat (Wylie and 

Casazza 2001; Wylie et al. 2003b, 2004b). 

Other land use practices also currently threaten the survival of the snake. Nonnative predators, 

including introduced predatory game fish, bullfrogs, and domestic cats, can threaten snake populations 

(Dickert 2003; Wylie et al. 1996; Wylie et al. 2003c). Nonnative competitors, such as the introduced 

water snake (Nerodia fasciata) in the American River and associated tributaries near Folsom, may also 
Stone Lakes NWR Comprehensive Conservation Plan 251

threaten the giant garter snake (Stitt et al. 2005). Recreational activities, such as fishing, may disturb 

snakes and disrupt basking and foraging activities. While large areas of seemingly suitable snake 

habitat exist in the form of duck clubs and waterfowl management areas, water management of these 

areas typically does not provide the summer water needed by the species. Degraded water quality 

continues to be a threat to the species both on and off refuges. 

The disappearance of giant garter snakes from much of the west side of the San Joaquin Valley was 

approximately contemporaneous with the expansion of subsurface drainage systems in this area, 

providing circumstantial evidence that the resulting contamination of ditches and sloughs with drain 

water constituents (principally selenium) may have contributed to the demise of giant garter snake 

populations. Dietary uptake is the principle route of toxic exposure to selenium in wildlife, including 

giant garter snakes (Beckon et al. 2003). Many open ditches in the northern San Joaquin Valley carry 

subsurface drainwater with elevated concentrations of selenium. Green sunfish (Lepomis cyanellus) in 

this drainwater have been found to have concentrations of selenium ranging from 12 to 23 μp/g (Saiki 

1998), within the range of concentrations associated with adverse affects on predator aquatic reptiles 

(Hopkins et al. 2002). Since 1996, subsurface drainwater has been discharged, via the Grassland 

Bypass Project into Mud Slough North, where selenium concentrations in small fish, including 

mosquito fish, frequently reach 10-15 μp/g (Beckon et al. 2003).

The Central Valley contains a number of endangered ecosystems due to its fertile soils, amiable 

climates, easy terrains, and other factors that historically have encouraged human settlement and 

exploitation (Noss et al. 2003). Environmental impacts associated with urbanization include loss 

of biodiversity and habitat, alternation of natural fire regimes, fragmentation of habitat from road 

construction, and degradation due to pollutants (Service 1999). Rapidly expanding cities within the 

snake’s range include Chico, Yuba City, the Sacramento area, Galt, Stockton, Gustine, and Los Banos.

The draft recovery plan for the snake subdivided its historic range into four recovery units (Service 

1999). These are: (1) the Sacramento Valley unit, extending from the vicinity of Red Bluff south 

to the confluence of the Sacramento and Feather Rivers; (2) the Mid-Valley unit, extending from the 

American and Yolo Basins south to Duck Creek near the City of Stockton; (3) the San Joaquin Valley 

unit, extending south from Duck Creek to the Kings River; and (4) the South Valley unit, extending 

south from the Kings River to the Kern River Basin. The Refuge is located in the Mid-Valley unit.

Currently, only the Sacramento Valley Recovery Unit, at the northern end of the species’ range, is 

known to support relatively large, stable populations of the snake. This unit contains three populations: 

Butte Basin, Colusa Basin, and Sutter Basin, which includes the Gilsizer Slough and Robbins area 

subpopulations. This recovery unit includes a large amount of suitable habitat, both in protected areas 

on state refuges and refuges of the Sacramento NWR Complex in the Colusa and Sutter Basins, and 

along waterways associated with rice farming (Service 1999). While populations within the unit have 

some protection on refuge and other public lands, such as the Colusa NWR, Delevan NWR, and Sutter 

NWR, snakes are subject to flooding and mortality from predatory fish and birds, vehicular traffic, 

agricultural practices, and maintenance of water channels. The populations within this unit are widely 

distributed and mostly restricted to unnatural agricultural delivery and drainage facilities associated 

with rice fields, and habitat corridors connecting populations or subpopulations are not present and/or 

protected. 

The Mid-Valley Recovery Unit, directly to the south of the Sacramento Valley Recovery Unit, 

includes seven populations: American Basin, Yolo Basin-Willow Slough, Yolo Basin-Liberty Farms, 

Sacramento Area, Badger Creek/Willow Creek, Caldoni Marsh, and East Stockton. The status of 

the seven snake populations in the Mid-Valley Recovery Unit is very uncertain. The East Stockton 

population may be extirpated, and is not considered recoverable as a result of urban encroachment into 

habitat (Service 1999). Five of the remaining six populations within this recovery unit are very small, 

highly fragmented and isolated, and, except for the Badger Creek/Willow Creek population, are also 

threatened by urbanization. This latter population is within a small isolated area. Within this recovery 

unit, only the American Basin population supports a sizeable snake population, which is largely 
252 Stone Lakes NWR Comprehensive Conservation Plan

dependent upon rice lands. The American 

Basin population, although threatened by urban development, receives protection from the approved 

Metro Air Park HCP and the Natomas Basin HCP, which share a regional strategy to maintain a viable 

snake population in the basin. 

The remaining two recovery units are located to the south in the San Joaquin Valley, where the best 

available data indicates that the snake’s status is precarious. The San Joaquin Valley Recovery Unit 

contains three historic snake populations: North and South Grasslands; Mendota Area; and Burrell/

Lanare Area (Service 1999). This recovery unit formerly supported large snake populations, but 

numbers have declined severely in recent decades, and recent survey efforts indicate that numbers are 

very low compared to Sacramento Valley populations. No surviving snake populations are known 

from the fourth recovery unit, the South Valley Recovery Unit, at the southern end of the snake’s 

historic range. This unit includes only extirpated populations, including the historic but lost habitats of 

Tulare Lake and Buena Vista Lake.

Since 1995, BRD has been studying life history and habitat requirements of the giant garter snake 

within a few of the 13 populations identified in the 1993 listing. BRD has studied snake subpopulations at the Sacramento, Delevan, and Colusa NWRs and in the Colusa Basin Drain within the 

Colusa Basin, at Gilsizer Slough within the Sutter Basin, at the Badger Creek area of the Cosumnes 

River Preserve within the Badger Creek/Willow Creek area of the Delta Basin, and in the Natomas 

Basin within the American Basin (Hansen 2003, 2004; Wylie 1998a, 1998b, 2003; Wylie et al. 1996; 

Wylie et al. 2000; Wylie et al. 2002; Wylie et al. 2003a, 2004a; Wylie et al. 2003b, 2004b). These 

areas contain the largest extant giant garter snake sub-populations. However, outside of protected 

areas, snakes are still subject to all threats identified in the final rule. The other sub-populations are 

distributed discontinuously in small, isolated patches, and are vulnerable to extirpation by stochastic 

environmental, demographic, and genetic processes (Goodman 1987a). 

Until recently, there were no post-1980 sightings of giant garter snakes from Stockton southward, and 

surveys of historic localities conducted in 1986 did not detect any snakes (Hansen 1988). Since 1995, 

however, surveys conducted by CDFG in cooperation with BRD around Los Banos and the Volta 

Wildlife Area in the Grasslands, and Mendota Wildlife Area in the Mendota Area have detected snakes, 

but in numbers much lower than those found in Sacramento Valley sub-populations (Dickert 2002, 

2003; Williams and Wunderlich 2003; Wylie 1998a). The estimated total population size for the Volta 

Wildlife Area is 45 individuals, approximately only 5.6 snakes per mile (3.5 snakes per kilometer). 

Such low numbers are illustrative of a tenuously small snake population. Also, one-third of the giant 

garter snakes found had lumps on their bodies suggestive of a parasitic nematode infection (Dickert 

2003); further study is underway. However, ten of the 31 snakes found in 2003 weighed less than 40 

grams, indicating that giant garter snakes have been breeding at the Volta Wildlife Area. These results 

demonstrate that giant garter snakes are still extant in the northern San Joaquin Valley, but probably in 

extremely low numbers/densities. All sub-populations are isolated from each other with no protected 

dispersal corridors. Few opportunities for re-colonization of small sub-populations that may become 

extirpated exist given the isolation from larger populations and lack of dispersal corridors between 

them. 

The draft recovery criteria require multiple, stable sub-populations within each of the three recovery 

units, with sub-populations well-connected by corridors of suitable habitat. This entails that corridors 

of suitable habitat between existing snake sub-populations be maintained or created to enhance subpopulation interchange to offset threats to the species (Service 1999). Currently, only the Northern 

Sacramento Valley Recovery Unit is known to support relatively large, stable giant garter snake 

populations. Habitat corridors connecting sub-populations, even in the Northern Sacramento Valley 

Recovery Unit, are either not present or not protected. Overall, the future availability of habitat in the 

form of canals, ditches, and flooded fields are subject to 

market-driven crop choices, agricultural practices, and urban development, and are, thus, uncertain and 
Stone Lakes NWR Comprehensive Conservation Plan 253

unpredictable. 

A number of State, local, private, and unrelated Federal actions have occurred within or near the action 

area, affecting the environmental baseline of the giant garter snake. Some of these projects have 

been subject to prior section 7 consultation. These actions have resulted in both direct and indirect 

effects to snake habitat within the region. Ongoing agricultural activities also affect the environmental 

baseline for the snake, and are largely not subject to section 7 consultation. Some agriculture, such 

as rice farming, can provide valuable seasonal foraging and upland habitat for the snake. Although 

rice fields and agricultural waterways can provide habitat for the snake, agricultural activities such as 

waterway maintenance, weed abatement, rodent control, and discharge of contaminants into wetlands 

and waterways can degrade snake habitat and increase the risk of snake mortality (Service 1999). 

Ongoing maintenance of agricultural waterways can also eliminate or prevent establishment of snake 

habitat, eliminate food resources for the snake, and can fragment existing habitat and prevent dispersal 

of snakes (Service 1999). Flood control and maintenance activities which can result in snake mortality 

and degradation of habitat include levee construction, stream channelization, and the rip-rapping of 

streams and canals (Service 1999). Numerous development projects have been constructed in or near 

snake habitat in this rapidly urbanizing area. Remaining populations are vulnerable to secondary 

effects of urbanization, such as increased predation by house cats and increased vehicular mortality. 

Most documented occurrences of giant garter snakes in this area of Sacramento County have been 

adversely impacted by development, including freeway construction, flood control projects, and 

commercial development.

Giant garter snakes have been documented on or adjacent to sites that will be affected by the proposed 

action. The snake has been documented at Beach Lake, South Stone Lake, Snodrass Slough, and 

along the Cosumnes River corridor, southwest of the refuge project boundary (California Natural 

Diversity Database 2005). These occurrences make up part of the Sacramento Basin subpopulation. 

A survey conducted by Dr. Glen Wylie, Biological Resources Division (BRD) of the U.S. Geological 

Survey, on SLNWR during the summer of 1997 and subsequent informal surveys by refuge staff have 

failed to document the presence of giant garter snake on the Refuge. However, these surveys were 

not conducted at a level of intensity sufficient to prove absence. Therefore, the current status of this 

species within the Refuge boundary and in the action area is unclear. Because the Refuge has little 

upland refugia, Dr. Wylie concluded that snake populations in the area may have been severely reduced 

by the prolonged flooding during January 1997, and that snake populations have not had sufficient time 

to recover. However, the Refuge contains suitable habitat to support the snake and provides the largest 

remaining parcel of snake habitat in this subpopulation. 

Valley Elderberry Longhorn Beetle

The valley elderberry longhorn beetle was federally listed as a threatened species on August 8, 1980 

(Service 1980). Critical habitat for the beetle was designated on the same date. Two areas along the 

lower American River in the Sacramento metropolitan area have been designated as critical habitat 

for the beetle–one along the American River at Goethe and Ancil Hoffman parks (American River 

Parkway Zone) about 10 miles upstream from the river’s mouth and the second is at the Sacramento 

Zone, an area about 2 miles upstream from the river’s mouth and about 0.5-mile northeast of the river’s 

right-bank (downstream aspect) levee. In addition, an area along Putah Creek in Solano County and 

an area west of Nimbus Dam along the American River Parkway, Sacramento County are designated 

as essential habitat in the Valley Elderberry Longhorn Beetle Recovery Plan (Service 1984). Each of 

these areas is known to support large numbers of mature elderberry shrubs with evidence of beetle use. 

The beetle depends on its host plant, the elderberry shrub (Sambucus spp.). Elderberries are locally 

common components of the remaining riparian forest and savannah landscapes, and to a lesser extent 

the mixed chaparral-foothill woodlands, of the Central Valley. Use of elderberry shrubs plants by the 

beetle, a wood borer, is rarely apparent. Frequently, the only exterior evidence of the shrub’s use by 
254 Stone Lakes NWR Comprehensive Conservation Plan

the beetle is an exit hole created by the larva emerging just prior to the pupae stage. Observations 

of elderberry shrubs along the Cosumnes River and in the Folsom Lake area indicate that larval 

beetles can be found in elderberry stems with no apparent exit holes; the larvae either succumb prior 

to constructing an exit hole or are not developed sufficiently to construct one. Larvae appear to be 

distributed in stems which are one inch or greater in diameter at ground level and can occur within both 

living and dead stems. The Valley Elderberry Longhorn Beetle Recovery Plan (Service 1984) and Barr 

(1991) further describe the beetle’s life history.

Beetle densities are probably naturally low (Service 1984); and it has been suggested, based on the 

spatial distribution of occupied shrubs (Barr 1991), that the beetle is a poor disperser. Low density and 

limited dispersal capability result in high vulnerability to the negative effects of habitat fragmentation 

and the resulting isolation of small sub-populations. 

When the beetle was initially listed as threatened, the species was known from less than ten localities 

along the American and Merced rivers, and Putah Creek. By completion of the Valley Elderberry 

Longhorn Beetle Recovery Plan in 1984, additional species localities had been found along the 

American River and Putah Creek. The California Natural Diversity Data Base (CNNDB 2005) records 

191 occurrences for this species in 23 counties throughout the Central Valley, from a location along 

the Sacramento River in Shasta County southward to an area along Caliente Creek in Kern County. 

Although the beetle continues to be threatened by long-term habitat loss and fragmentation due to 

extensive urbanization and land-use conversions throughout its range, there are relatively new threats 

as well, including destruction by non-native Argentine ants (Linepithema humile), mortality due to 

pesticide drift, competition due to exotic plant invasions, and the various adverse effects arising from 

livestock grazing. 

Habitat loss has been ranked as the single greatest threat to biodiversity in the United States (Wilcove 

et al. 1998). In the 1980 final rule to list the beetle as threatened, habitat destruction was cited as the 

primary factor contributing to the need to federally list the species. As described in the final rule, 

by the time the species was listed, its habitat had largely disappeared throughout much of its former 

range, due to such factors as agricultural conversions, levee construction, and stream channelization. 

The 1984 recovery plan reiterated the primary threats to the beetle as: loss and alteration of habitat 

by agricultural conversions; grazing; levee construction; stream and river channelization; removal 

of riparian vegetation; riprapping of shorelines; and recreational, industrial and urban development 

(Service 1984). 

Riparian forests, the primary habitat for the beetle, have been severely depleted throughout the Central 

Valley over the last two centuries as a result of expansive agricultural and urban development (Katibah 

1984; Thompson 1961; Roberts et al. 1977). Since human colonization, these forests have been “...

modified with a rapidity and completeness matched in few parts of the United States” (Thompson 

1961). As of 1849, the rivers and larger streams of the Central Valley were still largely undisturbed, 

supporting continuous bands of riparian woodland 4-5 miles in width along some major drainages 

such as the lower Sacramento River and generally about two miles wide along the lesser streams 

(Thompson 1961). Most of the riverine floodplains supported riparian vegetation to about the 100-year 

flood elevation level (Katibah 1984). A large human population influx after 1849, however, resulted 

in Central Valley riparian habitat being rapidly converted to agriculture and used as a source of wood 

for fuel and construction over a wide area (Thompson 1961). By 1868, riparian woodland had already 

been severely impacted in the Central Valley, as evidenced by the following excerpt:

“This fine growth of timber which once graced our river (Sacramento), tempered the 

atmosphere, and gave protection to the adjoining plains from the sweeping winds, has 

entirely disappeared - the woodchopper’s axe has stripped the river farms of nearly 

all the hard wood timber, and the owners are now obliged to rely upon the growth of 

willows for firewood.” (Cronise 1868, in Thompson 1961). 
Stone Lakes NWR Comprehensive Conservation Plan 255

The clearing of riparian forests for fuel and construction also made this land available for agriculture 

(Thompson 1977). Natural levees bordering the rivers, once supporting vast tracts of riparian 

habitat, became prime agricultural land (Thompson 1961, 1977). As agriculture expanded in the 

Central Valley, needs for increased water supply and flood protection spurred water development and 

reclamation projects. Artificial levees, river channelization, dam building, water diversion, and heavy 

groundwater pumping further reduced riparian habitat to small, isolated fragments (Katibah 1984). 

In recent decades, these riparian areas have continued in decline, as a result of ongoing agricultural 

conversion as well and urban development and stream channelization. As of 1989, there were over 

100 dams within the Central Valley drainage basin and thousands of miles of water delivery canals and 

streambank flood control projects for irrigation, municipal and industrial water supplies; hydroelectric 

power; flood control; navigation; and recreation (Frayer et al. 1989). As a result, much of the riparian 

forests in the Central Valley have dwindled to discontinuous, unconnected narrow strips with widths 

measurable in feet compared to the former miles. 

By some estimates the Sacramento Valley once supported about 775,000-800,000 acres of riparian 

forest as recently as 1848 (Smith 1977; Katibah 1984). No comparable estimates are available for 

the San Joaquin Valley. Based on early soil maps, more than 921,000 acres of riparian habitat are 

estimated to have been present throughout the Central Valley under pre-settlement conditions (Katibah 

1984). Another source estimates that of approximately 5.0 million acres of wetlands in the Central 

Valley in the 1850s, about 1.6 million acres were riparian wetlands (Warner 1985; Frayer et al. 1989). 

Based on a CDFG riparian vegetation distribution map, by 1979 there were about 102,000 acres of 

riparian vegetation remaining in the Central Valley. This represents a decline in acreage of about 89 

percent as of 1979 (Katibah 1984). Significant losses were also estimated by Frayer et al. (1989), who 

reported that woody riparian forests in the Central Valley had declined to 34,600 acres by the mid1980s (from 65,400 acres in 1939). These studies document the dramatic historic loss trend of riparian 

habitat in the Central Valley in general. Because elderberry shrubs are a key component of riparian 

habitat, it is a reasonable conclusion that loss of beetle habitat has been equally as dramatic. 

A number of studies have focused on riparian loss along the Sacramento River, which supports some 

of the densest known populations of the beetle. About 98 percent of the middle Sacramento River’s 

historic riparian vegetation is estimated to have been extirpated by 1977 (California Department of 

Water Resources, 1979). It has been estimated that native riparian habitat along the Sacramento River 

from Redding to Colusa decreased from 27,720 acres to 18,360 acres (34 percent) in just two decades 

from 1952 and 1972 (McGill 1975; Conrad et al. 1977). The average rate of riparian loss on the middle 

Sacramento River was 430 acres per year during this two-decade period and 410 acres per year from 

1972 to 1977. In 1987, riparian areas as large as 180 acres were observed to have been converted to 

orchards along this river reach (McCarten and Patterson 1987). 

There is no comparable information on the historic loss of beetle habitat in non-riparian situations, 

such as elderberry savanna and other vegetation communities where elderberry occurs (e.g., oak or 

mixed chaparral-woodland, or grasslands, adjacent to riparian habitat). However, all natural habitats 

throughout the Central Valley have been heavily impacted within the last 200 years (Thompson 1961) 

and we can therefore assume that non-riparian beetle habitat also has suffered a widespread decline. 

This analysis focuses on loss of riparian habitat, because the beetle is primarily dependent upon 

riparian habitat. Nevertheless, adjacent upland areas are also likely to be important for the species, 

but this upland habitat typically consist of oak woodland or elderberry savanna bordering willow 

riparian habitat (Barr 1991). The riparian acreage figures given by Frayer et al. (1989) and Katibah 

(1984) included the oak woodlands concentrated along major drainages in the Central Valley and 

therefore probably included lands we would classify as upland habitat for the beetle adjacent to riparian 

drainages.

Between 1980 and 1995, the human population grew in the Central Valley by approximately 50 

percent, while the remainder of California grew by 37 percent. The Central Valley’s population totaled 
256 Stone Lakes NWR Comprehensive Conservation Plan

4.7 million by 1999, and it is expected to more than double again by 2040. The American Farmland 

Trust estimates that by 2040 more than one million cultivated acres will be lost and 2.5 million more 

put at risk (Ritter 2000) through urbanization related to population growth. The rapidly expanding 

human population of the Central Valley will likely result in continued pressure on riparian habitat, 

related elderberry shrubs, and the beetle. As evidence, the SFWO presently receives a number of 

requests each month for consultation on the beetle under section 7 of the Endangered Species Act.

While habitat loss is clearly a large factor leading to the species decline, other factors may also pose 

significant long-term threats to the beetle’s survival. Only about 20 percent of riparian sites with 

elderberries observed by Barr (1991) and Collinge et al. (2001) support beetle populations (Barr 1991; 

Collinge et al. 2001). Jones and Stokes (1988) found that only 65 percent of 4,800 riparian acres on 

the Sacramento River had evidence of beetle presence. The fact that a large percentage of apparently 

suitable habitat is unoccupied suggests that the beetle is limited by other factors such as its limited 

dispersal ability, habitat quality, or habitat fragmentation.

Massive destruction of riparian habitat in central California has clearly resulted in not only a loss of 

acreage, but severe habitat fragmentation. Fahrig (1997) indicated that habitat fragmentation becomes 

most important for those habitats that have suffered greater than 80 percent loss. Riparian habitat in 

the Central Valley, which has experienced greater than 90 percent loss by most estimates, exceeds this 

criterion. Existing data suggests that beetle populations are affected by such habitat fragmentation. 

Barr (1991) found that small, isolated habitat remnants were less likely to be occupied by beetles than 

larger patches, indicating that beetle sub-populations are often extirpated from small remaining habitat 

fragments. Moreover, Barr (1991) and Collinge 

et al. (2001) consistently found beetle exit holes occurring in clumps of elderberry bushes rather than 

isolated bushes, suggesting that isolated shrubs are less viable host habitat for this species.

Habitat fragmentation can be an important factor contributing to a species decline because: (1) it 

divides a large population into two or more small populations that become more vulnerable to direct 

loss, inbreeding depression, genetic drift, and other problems associated with small populations; (2) it 

limits a species potential for dispersal and colonization; and, (3) it makes habitat more vulnerable to 

outside influences by increasing the edge: interior ratio (Primack 1998). 

Small, isolated sub-populations are susceptible to extirpation from random demographic, 

environmental or genetic events (Shaffer 1981, Lande 1988, Primack 1998). While a large area may 

support a single large population, the smaller sub-populations that result from habitat fragmentation 

may not be large enough to persist over the long-term. As a population becomes smaller, it tends to 

lose genetic variability through genetic drift, leading to inbreeding depression and a lack of adaptive 

flexibility. Smaller populations also become more vulnerable to random fluctuations in reproductive 

and mortality rates, and are more likely to be extirpated by random environmental factors. 

Species that characteristically have small population sizes, such as large predators or habitat specialists, 

are more likely to become extinct than species that typically have large populations (Primack 1998). 

Also, a species with low population density (few individuals per unit area) tends to have only small 

populations remaining if its habitat is fragmented. Populations of species that naturally occur at lower 

density become extinct more rapidly than do those of more abundant species (Bolger et al. 1991). The 

species may be unable to persist within each fragment and thus gradually dies out across the landscape. 

The beetle, a specialist on elderberry plants, tends to have small population sizes, and occurs in low 

densities (Barr 1991; Collinge et al. 2001). Collinge et al. (2001) compared resource use and density 

of exit holes between the beetle and a related subspecies, the California elderberry longhorn beetle 

(Desmocerus californicus californicus). The valley elderberry longhorn beetle tended to occur in 

areas with higher elderberry densities, but had lower exit hole densities than the California elderberry 

longhorn beetle. With extensive riparian habitat loss and fragmentation, these naturally small 

populations are broken into even smaller, isolated populations. Once a small population has been 
Stone Lakes NWR Comprehensive Conservation Plan 257

extirpated from an isolated habitat patch, the species may be unable to re-colonize this patch. Insects 

with limited dispersal and colonization abilities may persist better in large habitat patches than small 

patches because small fragments may be insufficient to maintain viable populations and the insects may 

be unable to disperse to more suitable habitat (Collinge 1996). 

Some studies suggest that the beetle is unable to recolonize drainages where the species has been 

extirpated, because of its limited dispersal ability (Huxel 2000; Barr 1991; Collinge et al. 2001). Huxel 

and Collinge (2001) used computer simulations of colonization and extinction patterns for the beetle 

based on differing dispersal distances and found that the short dispersal simulations best matched 

the 1997 census data in terms of site occupancy. This suggests that in natural-systems, dispersal 

recolonization is limited to nearby sites. At spatial scales greater than ten kilometers, such as across 

drainages, beetle occupancy appears to be strongly influenced by regional extinction and colonization 

processes, and colonization is constrained by limited dispersal (Collinge et al. 2001). 

Except for one occasion, drainages examined by Barr (1991) that were occupied in 1991 remained 

occupied in 1997 (Collinge et al. 2001). The one exception was Stoney Creek, which was occupied 

in 1991, but not in 1997. All drainages found by Barr (1991) to be unoccupied in 1991 were also 

unoccupied in 1997. This data suggests that drainages unoccupied by the beetle remain unoccupied.

In addition, recent evidence indicates that the invasive Argentine ant poses a risk to the long-term 

survival of the beetle. Surveys along Putah Creek found beetle presence where Argentine ants were 

not present or had recently colonized, but the beetle was absence from otherwise suitable sites where 

Argentine ants had become well-established (Huxel 2000). The Argentine ant has already negatively 

impacted populations of other native arthropod species (Holway 1998; Ward 1987). Predation on eggs, 

larvae, and pupae are the most likely impacts these ants have on the beetle. In Portugal, Argentine 

ants have been found to be significant egg predators on the eucalyptus borer, a cerambycid similar to 

the beetle. Egg predation on the beetle could lead to local extirpations, as indicated by a population 

viability study suggesting that egg and juvenile mortality are significant factors affecting probability of 

extinction for the beetle (Huxel and Collinge, 2001). The Argentine ant has been expanding its range 

throughout California since its introduction around 1907, especially in riparian woodlands associated 

with perennial streams (Holway 1998; Ward 1987). Huxel (2000) concluded that, given the potential 

for Argentine ants to spread with the aid of human activities such as movement of plant nursery stock 

and agricultural products, this species may come to infest most drainages in the Central Valley along 

the valley floor, where the beetle is found. 

Another potential harmful factor for the beetle is direct spraying with pesticides and related pesticide 

drift. A wide range of such spraying is done to control mosquitoes, crop diseases, and undesirable 

plants and insects. Although there have been no studies specifically focusing on the direct and indirect 

effects of pesticides on the beetle, evidence suggest that the species may be adversely affected by 

some pesticide applications. As of 1980, the prevalent land-use adjacent to riparian habitat in the 

Sacramento Valley was agriculture, even in regions where agriculture was historically not generally 

the most common land use (Katibah et al. 1984), therefore the species is likely vulnerable to pesticide 

contamination from an array of agricultural pesticide application practices. Recent studies of major 

rivers and streams documented that 96 percent of all fish, 100 percent of all surface water samples, 

and 33 percent of major aquifers contained one or more pesticides at detectable levels (Gilliom 1999). 

Pesticides were identified as one of the 15 leading causes of impairment for streams included on 

the Clean Water Act section 303(d) lists of impaired waters. Because the beetle occurs primarily in 

riparian habitat, the contamination of rivers and streams likely has affects on this species and its habitat. 

Pesticides have been identified as one of a number of potential causes of the decline of pollinator 

species and other insects beneficial to agriculture (Ingraham et al. 1996); therefore, it is likely that the 

beetle, typically occurring adjacent to agricultural lands, is adversely affected by the use of pesticides.

Also, competition from invasive exotic plants, such as giant reed (Arundo donax), negatively affects 

riparian habitat supporting the beetle. Giant reed, a native of Asia, has become a serious problem in 
258 Stone Lakes NWR Comprehensive Conservation Plan

California riparian habitats, forming dense, homogenous stands essentially devoid of wildlife. Giant 

reed can grow up to 2.5 inches per day and yield 8.3 tons of oven-dry cane per acre; it also tolerates 

drought, floods, and extreme temperatures, and is not significantly affected by insects, disease, 

herbivory, fire, or mechanical disturbance. It has an extensive root system allowing it to resprout 

rapidly after any disturbance and it easily out-competes native riparian vegetation. Giant reed also 

introduces a frequent fire cycle into the riparian ecosystem, disrupting natural riparian dynamics and 

eventually forming homogenous climax communities. Although giant reed has become extensively 

distributed throughout the Central Valley and along its waterways, the extent to which it has negatively 

affected elderberries and the beetle is not specifically known.

Another potential factor in the decline of the beetle is the effects of adverse livestock grazing practices, 

which can result in the destruction of entire elderberry plants and inhibition of elderberry regeneration. 

Cattle, sheep, and goats readily forage on new elderberry growth, and goats will consume even decadent 

growth. Well-manicured stands of elderberries, which often occur due to livestock grazing, have 

generally been shown to have a relative absence of beetles (Service 1984). The effects on the beetle of 

both grazing and exotic plant invasions are likely significantly exacerbated by the problem of habitat 

fragmentation of elderberries. Such fragmentation increases the edge: interior ratio of habitat patches, 

thereby facilitating the adverse effects of these outside influences. 

The beetle has been recorded adjacent to the Refuge boundary, along the Cosumnes River corridor 

(Tom Harvey, pers. comm.). The beetle occurs in elderberry shrubs in riparian habitats and in open 

savannahs with oaks and cottonwoods. Biannual surveys have been conducted on the elderberries on 

the Beach Lake Unit, and no exit holes have been confirmed to date. The majority of elderberries on the 

Refuge (95%) are less than 3 years old and are not of a sufficient size for the beetles. Elderberry shrubs 

have been introduced on the Refuge in two locations; on the Lewis property and near an abandoned 

homestead on the North Stone Lake property. To date, the beetle has not been recorded within the 

Refuge; however, suitable habitat exists within the boundary at the Bufferlands for the Sacramento 

Regional Wastewater Treatment Plant, at North and South Stone Lakes, and along Snodgrass Slough. 

Vernal Pool Tadpole Shrimp and Vernal Pool Fairy Shrimp

The vernal pool tadpole shrimp and vernal pool fairy shrimp were listed as endangered and threatened, 

respectively, on September 19, 1994 (Service 1994). The final rule to designate critical habitat for 

15 vernal pool species, including two crustaceans, was published on August 6, 2003 (Service 2003), 

with further clarifications on critical habitat designations for listed vernal pool species published in an 

August 11, 2005, final rule (Service 2005 ). Further information on the life history and ecology of the 

vernal pool fairy shrimp and vernal pool tadpole shrimp may be found in the final listing rule, the final 

rule to designate critical habitat, Eng et al. (1990), Helm (1998), and Simovich et al. (1992), and the 

Recovery Plan for Vernal Pool Ecosystems of California and Southern Oregon (Service 2005). Critical 

habitat for vernal pool crustaceans is not present on the Refuge.

The vernal pool tadpole shrimp has dorsal compound eyes, an approximately one-inch long large shieldlike carapace that covers most of its body, and a pair of long cercopods at the end of its last abdominal 

segment (Linder 1952; Longhurst 1955; Pennak 1989). It is primarily a benthic animal that swims with 

its legs down. Vernal pool tadpole shrimp climb or scramble over objects, and plow along bottom 

sediments as they forage for food. Its diet consists of organic detritus and living organisms, such as 

fairy shrimp and other invertebrates (Pennak 1989; Fryer 1987). The females deposit their eggs on 

vegetation and other objects on the pool bottom. Tadpole shrimp eggs are known as cysts, and during 

the dry months of the year, they lie dormant in the dry pool sediments (Lanaway 1974; Ahl 1991).

The life history of the vernal pool tadpole shrimp is linked to the environmental characteristics of its 

vernal pool habitat. After winter rains fill the pools, its dormant cysts may hatch in as little as four days 

(Ahl 1991, Rogers 2001), and the animals may become sexually mature within three to four weeks 
Stone Lakes NWR Comprehensive Conservation Plan 259

after hatching (Ahl 1991; Helm 1998; King 1996). A portion of the cysts hatch immediately and the 

rest remain dormant in the soil to hatch during later rainy seasons (Ahl 1991). The vernal pool tadpole 

shrimp is a relatively long-lived species (Ahl 1991), and will generally survive for as long as its habitat 

remains inundated, sometimes for six months or more (Ahl 1991; Gallagher 1996; Helm 1998). Adults 

are often present and reproductive until the pools dry up in the spring (Ahl 1991; Gallagher 1996; 

Simovich et al. 1992).

Vernal pool tadpole shrimp are found only in ephemeral freshwater habitats, including alkaline pools, 

clay flats, vernal lakes, vernal pools, vernal swales, and other seasonal wetlands in California (Helm 

1998). The vernal pool tadpole shrimp is known from 221 occurrences in the Central Valley (CNDDB 

2005), ranging from east of Redding in Shasta County south to Fresno County, and from a single 

vernal pool complex located in the San Francisco Bay National Wildlife Refuge in Alameda County. 

It inhabits vernal pools containing clear to highly turbid water, ranging in size from 54 square feet in 

the Mather Air Force Base area of Sacramento County, to the 89-acre Olcott Lake at Jepson Prairie in 

Solano County; the potential ponding depth of occupied habitat ranges from 1.5 inches to 59 inches. 

Although vernal pool tadpole shrimp are found on a variety of geologic formations and soil types, 

Helm (1998) found that over 50 percent of vernal pool tadpole shrimp occurrences were on High 

Terrace landforms and Redding and Corning soils. Vernal pool tadpole shrimp are uncommon even 

where vernal pool habitat occurs (Service 2005). The largest concentration of vernal pool tadpole 

shrimp occurrences are found in the Southeastern Sacramento Valley Vernal Pool Region, as defined 

in the Service’s Recovery Plan for Vernal Pool Ecosystems of California and Southern Oregon (2005). 

In this vernal pool region, this species occurs on a number of public and private lands in Sacramento 

County, and from a few locations in Yuba and Placer Counties, including Beale Air Force Base. 

Vernal pool fairy shrimp have delicate elongate bodies, large stalked compound eyes, no carapace, and 

11 pairs of phyllopods, or gill-like structures that also serve as legs. Typically less than one-inch long, 

they swim or glide gracefully upside-down by means of complex, wavelike beating movements. Fairy 

shrimp feed on algae, bacteria, protozoa, rotifers, and detritus. The second pair of antennae in adult 

male fairy shrimp are greatly enlarged and specialized for clasping the females during copulation. The 

females carry eggs in an oval or elongate ventral brood sac. The eggs are either dropped to the pool 

bottom or remain in the brood sac until the female dies and sinks. The dormant cysts are capable of 

withstanding heat, cold, and prolonged desiccation, and they can remain viable in the soil for decades 

after deposition. When the pools refill in the same or subsequent seasons, some, but not all, of the 

cysts may hatch. The cyst bank in the soil may therefore be comprised of cysts from several years 

of breeding (Donald 1983). The early stages of the fairy shrimp develop rapidly into adults and may 

become sexually mature within two weeks after hatching (Gallagher 1996; Helm 1998). Such quick 

maturation permits populations to persist in short-lived shallow bodies of water (Simovich et al. 1992). 

In pools that persist for several weeks to a few months, fairy shrimp may have multiple hatches during 

a single season (Helm 1998; Gallagher 1996).

Vernal pool fairy shrimp are found only in ephemeral freshwater habitats, including alkaline pools, 

ephemeral drainages, rock outcrop pools, vernal pools, and vernal swales in California and Southern 

Oregon (Eriksen and Belk 1999). Occupied habitats range in size from rock outcrop pools as small 

as 11 square feet to large vernal pools up to 12 acres; the potential ponding depth of occupied habitat 

ranges from 1.2 inches to 48 inches. 

The vernal pool fairy shrimp is known from 372 occurrences extending from the Stillwater Plain in 

Shasta County through most of the length of the Central Valley to Pinnacles in San Benito County 

(Eng et al. 1990; Fugate 1992; Sugnet and Associates 1993; CNDDB 2005). Five additional, disjunct 

populations exist: one near Soda Lake in San Luis Obispo County; one in the mountain grasslands of 

northern Santa Barbara County; one on the Santa Rosa Plateau in Riverside County; one near Rancho 

California in Riverside County; and one on the Agate Desert near Medford, Oregon (CNDDB 2005; 

Helm 1998; Eriksen and Belk 1999; Service 2003). Three of these isolated populations each contain 

only a single pool known to be occupied by the vernal pool fairy shrimp. Although the vernal pool 
260 Stone Lakes NWR Comprehensive Conservation Plan

fairy shrimp is distributed more widely than most other fairy shrimp species, it is generally uncommon 

throughout its range and rarely abundant where it does occur (Eng et al. 1990; Eriksen and Belk 1999). 

The greatest number occurrences of the vernal pool fairy shrimp are in the Southeastern Sacramento 

Vernal Pool Region (Service 2005), where it is found in scattered vernal pool habitats in Placer, 

Sacramento, and San Joaquin Counties, in the vicinity of Beale Air Force Base in Yuba County, and at 

a single location in El Dorado County. 

Although the vernal pool fairy shrimp and the vernal pool tadpole shrimp are not often found in the 

same vernal pool at the same time, when coexistence does occur, it is generally in deeper, longer lived 

pools (Eng et al. 1990; Thiery 1991; Gallagher 1996). In larger pools, vernal pool crustacean species 

may be able to coexist by utilizing different physical portions of the vernal pool or by eating different 

food sources (Daborn 1978; Mura 1991; Thiery 1991), or by hatching at different temperatures or 

developing at different rates (Thiery 1991; Hathaway and Simovich 1996). 

The primary historic large-scale dispersal method for the vernal pool tadpole shrimp and vernal pool 

fairy shrimp likely was large scale flooding resulting from winter and spring rains which allowed 

colonization of different individual vernal pools and other vernal pool complexes (King 1996). This 

dispersal is currently non-functional due to the construction of dams, levees, and other flood control 

measures, and widespread urbanization within significant portions of the range of this species. 

Waterfowl and shorebirds may now be the primary dispersal agents for vernal pool tadpole shrimp 

and vernal pool fairy shrimp (King 1996; Simovich et al. 1992). The eggs of these branchiopods are 

either ingested (Krapu 1974; Swanson et al. 1974; Driver 1981; Ahl 1991) and/or adhere to the legs and 

feathers where they are transported to new habitats. Cysts may also be dispersed by a number of other 

species, such as cattle and humans (Eriksen and Belk 1999).

At the local level, vernal pool crustaceans are often dispersed from one pool to another through surface 

swales that connect one vernal pool to another. These dispersal events allow for genetic exchange 

between pools and create a population of animals that extends beyond the boundaries of a single pool. 

These dispersal events also allow vernal pool crustaceans to move into pools with a range of sizes and 

depths. In dry years, vernal pool crustaceans may only hatch in the largest and deepest pools. In wet 

years, vernal pool crustaceans may be present in all pools. The movement of vernal pool crustaceans 

into vernal pools of different sizes and depths allows these species to survive the environmental 

variability that is characteristic of their habitats.

The genetic characteristics of these species, as well as ecological conditions, such as watershed 

continuity, indicate that populations of vernal pool crustaceans are defined by pool complexes 

rather than by individual vernal pools (Fugate 1992). Therefore, the most accurate indication of the 

distribution and abundance of these species is the number of inhabited vernal pool complexes. The 

pools and, in some cases, pool complexes supporting these species may be small. Human-caused 

and unforeseen natural catastrophic events such as long-term drought, non-native predators, off-road 

vehicles, pollution, berming, and urban development, threaten their extirpation at some sites. Vernal 

pool fairy shrimp and vernal pool tadpole shrimp continue to be threatened by all of the factors which 

led to the original listing of this species, primarily habitat loss through agricultural conversion and 

urbanization (Service 2005).

The vernal pool tadpole shrimp and vernal pool fairy shrimp are imperiled by a variety of humancaused activities. Their habitats have been lost through direct destruction and modification due to 

filling, grading, disking, leveling, and other activities. In addition, vernal pools have been imperiled by 

a variety of anthropogenic modifications to upland habitats and watersheds. These activities, primarily 

urban development, water supply/flood control projects, land conversion for agriculture, off-road 

vehicle use, certain mosquito abatement measures, and pesticide/herbicide use can lead to disturbance 

of natural flood regimes, changes in water table depth, alterations of the timing and duration of vernal 

pool inundation, introduction of non-native plants and animals, and water pollution. These can result in 

adverse effects to vernal pool species. In addition to direct loss, the habitats of the vernal pool tadpole 
Stone Lakes NWR Comprehensive Conservation Plan 261

shrimp and the vernal pool fairy shrimp have been and continue to be highly fragmented throughout 

their ranges due to conversion of natural habitat for urban and agricultural uses. Fragmentation results 

in smaller isolated shrimp populations. Ecological theory predicts that such populations will be highly 

susceptible to extirpation due to chance events, inbreeding depression, or additional environmental 

disturbance (Gilpin and Soulé 1988; Goodman 1987a, 1987b). If an extirpation event occurs in a 

population that has been fragmented, the opportunities for re-colonization would be greatly reduced 

due to geographic isolation from other source populations. 

Historically, vernal pools and vernal pool complexes occurred extensively throughout the Sacramento 

Valley of California. However, conversion of vernal pools and vernal pool complexes has resulted in 

a 91 percent loss of vernal pool resources in California (State of California 2003d). By 1973, between 

60 and 85 percent of the area within the Central Valley that once supported vernal pools had been 

destroyed (Holland 1978). In subsequent years, threats to this habitat type have continued and resulted 

in a substantial amount of vernal pool habitat being converted for human uses in spite of Federal 

regulations implemented to protect wetlands. The U.S. Army Corps of Engineers (Corps) Sacramento 

District has several thousand vernal pools under its jurisdiction (Coe 1988), which includes most of the 

known populations of these listed species. Between 1987 and 1992, 467 acres of wetlands within the 

Sacramento area were filled pursuant to the Corps’ Nationwide Permit 26 (Service 1992). A majority 

of those wetland losses involved vernal pools, the endemic habitat of the vernal pool tadpole shrimp 

and the vernal pool fairy shrimp. King (1996) has estimated that approximately 15 to 33 percent of 

the original biodiversity of Central Valley vernal pool crustaceans has been lost since the 1800s. It is 

estimated that within 20 years human activities will destroy 60 to 70 percent of the remaining vernal 

pools (Coe 1988).

Sacramento County represents important, high quality habitat for the vernal pool tadpole shrimp and 

vernal pool fairy shrimp by providing large, nearly contiguous areas of relatively undisturbed vernal 

pool habitat. Sacramento County contains the greatest number of occurrences of vernal pool tadpole 

shrimp and also is one of the two counties with the greatest number of occurrences of vernal pool fairy 

shrimp. Sacramento County contains 60 (16 percent) out of the total of 372 reported occurrences of 

vernal pool fairy shrimp, and 60 (27 percent) out of the total of 221 reported occurrences of vernal 

pool tadpole shrimp (CNDDB 2005). Sugnet and Associates (1993) reported that of 3,092 “discrete 

populations” checked, only 345 locations, or about 11 percent of all locations checked, were found 

to support the vernal pool tadpole shrimp. Of these 345 locations supporting the vernal pool tadpole 

shrimp, 219 (63 percent) were in Sacramento County. Further, of the 3,092 locations checked, 178 

locations (6 percent) were found to support the vernal pool fairy shrimp. Of this total, 63 locations (35 

percent) were within Sacramento County. 

Throughout the Central Valley, approximately 13,000 acres of vernal pool habitats, including mitigation 

banks, have been set aside for the vernal pool fairy shrimp specifically as terms and conditions of 

section 7 consultations (Service 2005). In the Southeastern Sacramento Valley Vernal Pool Region, 

vernal pool fairy shrimp occurrences are protected from development at a number of private mitigation 

areas, compensation banks, private ranches with conservation easements, and the Beale Air Force 

Base in Yuba County. Very few actions have been taken specifically to benefit the vernal pool tadpole 

shrimp, although several Habitat Conservation Plans are developing vernal pool conservation plans in 

the region, including Sacramento and Placer Counties (Service 2005). 

The vernal pool tadpole shrimp and vernal pool fairy shrimp are imperiled by a variety of humancaused activities. Their habitats have been lost through direct destruction and modification due to 

filling, grading, disking, leveling, and other activities. In addition, vernal pools have been imperiled by 

a variety of anthropogenic modifications to upland habitats and watersheds. These activities, primarily 

urban development, water supply/flood control projects, land conversion for agriculture, off-road 

vehicle use, certain mosquito abatement measures, and pesticide/herbicide use, can lead to disturbance 

of natural flood regimes, changes in water table depth, alterations of the timing and duration of vernal 

pool inundation, introduction of non-native plants and animals, and water pollution. These indirect 
262 Stone Lakes NWR Comprehensive Conservation Plan

effects can result in adverse effects to vernal pool species.

The actions listed above have resulted in both direct and indirect impacts to vernal pools within 

the region, and have contributed to the loss of vernal pool tadpole shrimp and vernal pool fairy 

shrimp populations. Although a reduction of the two shrimp populations has not been quantified, 

the acreage of lost habitat continues to grow. On-going residential and commercial developments 

within the Sacramento County also affect the listed vernal pool crustaceans and their habitats. Human 

population growth in Sacramento County has steadily increased. For the period between 1990 and 

2000, population growth in Sacramento County increased 17.5 percent, with an average annual 

growth rate of 17.5 percent (State of California 2002). This annual growth appears to be increasing, 

as demonstrated by the 2.63 percent and 2.2 percent increases in population growth in 2001 and 2002, 

respectively (State of California 2003, 2003b). Increased housing demand and urban development 

accompany the population growth in Sacramento County. Between 1990 and 2000, housing units in 

Sacramento County increased by 1.37 percent annually (State of California 2000, 2003c). Population 

growth and concomitant housing demand and subsequent vernal pool resource development are 

projected to continue. Population projections for Sacramento County are expected to increase above 

2000 levels by 19.7 percent in 2010, by 28 percent in 2015, and by 37.5 percent in 2020 (State of 

California 2001).

A number of State, local, private, and unrelated Federal actions have occurred within the project area 

and adjacent region affecting the environmental baseline of these species. Some of these projects 

have been subject to prior section 7 consultation. Based on an informal review, the Service has 

issued approximately 177 biological opinions to Federal agencies on proposed projects in Sacramento 

County that have adversely affected the shrimp species since the two species were proposed to be 

listed in 1994. This total does not reflect the formal consultations that were withdrawn, those that 

were suspended, and those that have insufficient information to conclude an effects analysis, those that 

were amended, or ones that the Service issued a conference opinion. No State of California actions 

that have taken place within Sacramento County have adversely affected the species in the action area. 

Although these proposed projects in Sacramento County have eliminated vernal pools and vernal pool 

complexes, the associated conservation measures are designed to minimize the effects of proposed 

projects to these species. Thus, the trend for the two vernal pool crustaceans within Sacramento 

County is most likely downward.

Of the 136.5 acres of vernal pools that exist on Refuge managed lands, 16.5 acres, (12%) of vernal 

pools on the Refuge are naturally occurring pools, the rest are man-made mitigation pools (88%). The 

Wetland Preserve Unit, formerly known as AKT, contains 133.5 acres or 98% of vernal pools, and 

is managed under a conservation easement (SFWO file number 1-1-99-F-0118). This easement has 

periodically been surveyed (as required in the biological opinion) for vernal pool and other species 

for ten years, and vernal pool tadpole shrimp and vernal pool fairy shrimp have been documented 

within the easement area. Vernal pool fairy shrimp and vernal pool tadpole shrimp have also been 

documented in swales on the north Stone Lakes Unit. However, vernal pool crustaceans and other 

vernal pools species could potentially occur in any of the vernal pools, sloughs, or other passive 

seasonal wetlands managed by the Refuge.

Effects of the Proposed Action 

Giant garter snake 

Refuge activities, particularly construction activities (e.g., facilities construction and maintenance, 

habitat restoration), occurring in giant garter snake habitat may disturb, harass, injure, or kill giant 

garter snakes. Construction activities may remove vegetative cover and basking sites, fill or crush 

burrows, and decrease the prey base. Temporary dewatering of portions of canals or fields may 

temporarily remove giant garter snake habitat and may obstruct movement. Snakes may be killed or 
Stone Lakes NWR Comprehensive Conservation Plan 263

injured by construction equipment or other vehicles accessing the construction site. Disturbance from 

construction activities may also cause snakes to temporarily move into areas of unsuitable habitat 

where they may be more prone to higher rates of mortality from predation. Snakes may also be killed 

or injured by refuge, research, and visitor vehicles. Although operations and maintenance activities 

have the potential to harm individual giant garter snakes and cause short-term habitat alteration, there 

are long-term benefits to giant garter snakes due to increasing wetland acreage and riparian habitat and 

maintaining canals and wetlands. 

Recreational activities, such as fishing and hunting, may disturb snakes and disrupt basking and 

foraging activities. Increased vehicle use in giant garter snake habitat may harass, injure, or kill 

giant garter snakes. Vehicles will be used primarily on existing roads; therefore, harassment, injury, 

or mortality from vehicle use would occur only if snakes are in the roadway. Regarding the effects 

of the proposed use of pesticides, a Service-sponsored study indicated that the short-term effects of 

adulticides approved for mosquito control on the Refuge did not significantly reduce abundance or 

biomass of the snake’s prey items, macro-invertebrates and fish, in treated wetlands (Lawler et al.

1997). However, no information is available on the toxicity of pesticides directly to the giant garter 

snake. Without further information, it must be assumed that exposure of giant garter snakes to these 

chemicals could result in direct impacts, such as lethal or sub lethal effects to individual animals. 

Valley elderberry longhorn beetle 

The beetle has not been documented on the Refuge; however, it has been found adjacent to the refuge 

boundary along the Cosumnes River corridor and may be present in elderberry shrubs within the 

refuge boundary. The beetle and its habitat, the elderberry shrubs, may be affected by the proposed 

herbicides or pesticides if the chemicals come in contact with elderberry shrubs either by direct or 

indirect (drift, treated water inundation) contact. 

Though there are no documented occurrences of the beetle on the Refuge, however elderberry bushes 

are present. All existing elderberry shrubs are mapped and avoided during application of herbicides 

intended to control invasive weeds. The number of elderberry shrubs on the Refuge is small and 

relatively easy to avoid during the proposed pest management activities. The Refuge has planted and/

or maintained over 75 blue elderberries that may provide habitat for the Valley elderberry longhorn 

beetle. Plans for the Headquarters Unit include approximately 50 additional elderberry plants.

Management and restoration of riparian areas on the Refuge are expected to benefit the valley 

elderberry longhorn beetle. The SFWO expects that Refuge staff may remove or transplant a small 

number of shrubs. However, the Refuge has proposed to implement all guidelines listed in the 

Service’s July 1999, Conservation Guidelines for the Valley Elderberry Longhorn Beetle, therefore, 

potential adverse effects to the beetle and elderberry shrubs will be minimized. Trimming of 

elderberry shrubs that interfere with road and utility easements will be limited to the dormant period 

for the beetle whenever possible, thus minimizing the potential for take of the beetle.

Vernal pool fairy shrimp and vernal pool tadpole shrimp

Vernal pool fairy shrimp and vernal pool tadpole shrimp may be harmed, harassed, injured, or killed 

during surveys, monitoring, and management activities of vernal pool habitat. However, adherence 

to survey guidelines for vernal pool crustaceans will minimize the effects of surveys and monitoring 

activities on vernal pool crustaceans. The Refuge expects that information on presence and 

distribution of vernal pool crustaceans will assist the Refuge in improving management of vernal pool 

habitats.

Management of vernal pools using prescribed fire and grazing is expected to benefit vernal pool 
264 Stone Lakes NWR Comprehensive Conservation Plan

habitat by controlling proliferation of exotic plants. However, the effect of fire and grazing on vernal 

pool crustaceans is poorly known. It is expected that the use of fire and grazing may result in some 

disturbance and loss of cysts while benefiting and improving the long-term viability of vernal pool 

communities.

Cumulative Effects

Cumulative effects include the effects of future State, Tribal, local, or private actions that are 

reasonably certain to occur in the action area considered in this biological opinion. Future Federal 

actions that are unrelated to the proposed action are not considered in this section because they require 

separate consultation pursuant to section 7 of the Act. Our agency is aware of other projects currently 

under review by State, county, and local authorities where biological surveys have documented the 

occurrence of several listed species covered by this opinion. Projects under review include such 

actions as urban expansion, road improvement projects, water transfers that may not have a Federal 

nexus, and continued agricultural development. The cumulative effects of these known actions could 

pose a threat to the eventual recovery of the giant garter snake, valley elderberry longhorn beetle, and 

the vernal pool crustaceans.

An undetermined number of future land use conversions and routine agricultural practices are not 

subject to Federal permitting processes and may alter habitat or increase incidental take of giant garter 

snakes, valley elderberry longhorn beetles, vernal pool fairy shrimp, and vernal pool tadpole shrimp. 

These additional cumulative effects include 1) fluctuations in acres of aquatic habitat due to water 

management or acres of rice lands in production, 2) levee repairs, 3) dredging and clearing vegetation 

from irrigation canals, 4) mowing and clearing vegetation adjacent to canals and streams, 5) increased 

vehicular traffic on roads and levees, and 6) use of burrow fumigants. 

The vernal pool habitat for the vernal pool tadpole shrimp and vernal pool fairy shrimp also has been 

and continues to be increasingly fragmented throughout their ranges by conversion of natural habitat to 

urban, industrial, commercial, and agricultural uses. For all of these species, fragmentation results in 

small isolated populations. Ecological theory predicts that such populations will be highly susceptible 

to extirpation due to chance events, inbreeding depression, or additional environmental disturbance 

(Gilpin and Soule 1988, Goodman 1987a, b). Should an extirpation event occur in a population that 

has been fragmented, the opportunities for recolonization would be greatly reduced due to physical 

(geographical) isolation from other (source) populations.

Conclusion

After reviewing the current status of the following species; giant garter snake, valley elderberry 

longhorn beetle, vernal pool fairy shrimp, and vernal pool tadpole shrimp; the environmental baseline 

for the action area; the effects of Refuge management activities; and the cumulative effects, it is 

the Service’s biological opinion that Refuge management activities, as proposed, are not likely to 

jeopardize the continued existence of the above species. Critical habitat for the valley elderberry 

longhorn beetle has been designated in two areas in Sacramento County, California; however, this 

action does not affect those areas and, therefore, no destruction or adverse modification of its critical 

habitat is anticipated. Critical habitat for vernal pool fairy shrimp and vernal pool tadpole shrimp 

has been designated, but does not include the Refuge. No critical habitat has been designated for the 

remaining species; therefore, none will be affected.

INCIDENTAL TAKE STATEMENT

Section 9(a)(1) of the Act and Federal regulation pursuant to section 4(d) of the Act prohibit the take 

of endangered and threatened fish and wildlife species, respectively, without special exemption. Take 

is defined as harass, harm, pursue, hunt, shoot, wound, kill, trap, capture or collect, or to attempt to 

engage in any such conduct. Harass is defined by the Service as an intentional or negligent act or 
Stone Lakes NWR Comprehensive Conservation Plan 265

omission which creates the likelihood of injury to a listed species by annoying it to such an extent as to 

significantly disrupt normal behavioral patterns which include, but are not limited to, breeding, feeding, 

or sheltering. Harm is defined by the Service to include significant habitat modification or degradation 

that results in death or injury to listed species by impairing behavioral patterns including breeding, 

feeding, or sheltering. Incidental take is defined as take that is incidental to, and not the purpose 

of, the carrying out of an otherwise lawful activity. Under the terms of section 7(b)(4) and section 

7(o)(2), taking that is incidental to and not intended as part of the agency action is not considered to 

be prohibited taking under the Act provided that such taking is in compliance with this Incidental Take 

Statement. 

The measures described below are non-discretionary, and must be implemented by the agency so that 

they become binding conditions of any grant or permit issued to an applicant, as appropriate, in order 

for the exemption in section 7(o)(2) to apply. The Refuge has a continuing duty to regulate activities 

covered by this incidental take statement. If the Refuge (1) fails to adhere to the terms and conditions 

of the incidental take statement through enforceable terms that are added to any contract, agreement, or 

special use permit granted by the Refuge, and/or (2) fails to retain oversight to ensure compliance with 

these terms and conditions, the protective coverage of section 7(o)(2) may lapse.

Amount or Extent of Take

Giant garter snake

The SFWO anticipates incidental take of giant garter snakes will be difficult to detect or quantify for 

the following reasons: giant garter snakes are cryptically colored, secretive, and known to be sensitive 

to human activities. Snakes may avoid detection by retreating to burrows, soil crevices, vegetation, 

and other cover. Individual snakes are difficult to detect unless they are observed, undisturbed, at a 

distance. Most close-range observations represent chance encounters that are difficult to predict. It is 

not possible to make an accurate estimate of the number of snakes that would be harassed or harmed 

by Refuge operational activities described in the CCP. In instances when take is difficult to detect, the 

Service may estimate take in numbers of species per acre of habitat lost or degraded as a result of the 

action. Considering all permanent water sources (water that persists through summer) with a buffer of 

200 feet, the result is 2,069 acres of potential habitat. Permanent water sources include, lakes, sloughs, 

perennial marsh, managed permanent wetlands. Therefore, the Service anticipates that all snakes within 

the 2,069 acre area may be subject to harassment and harm as a result of implementation of the CCP. 

The SFWO anticipates that, while some take of giant garter snake may occur, the long-term results of 

the proposed management and restoration activities will benefit the snake and its habitat.

Valley elderberry longhorn beetle 

The SFWO is unable to quantify incidental take of the beetle, because the potential number of beetle 

larvae contained within each elderberry bush is unknown. Because it is not known how many larvae 

each stem can support, the SFWO must quantify the amount of incidental take of the beetle in terms of 

the number of plants and stems that would be lost. The SFWO anticipates that the amount of take for 

the beetle would be small due to the small number of elderberry shrubs on the Refuge and the proposed 

conservation measures for the species. Therefore, the SFWO anticipates that all beetles inhabiting 

not more than one elderberry plant with at least one stem measuring 1.0 inch or greater in diameter at 

ground level will be taken annually through harm, harassment, or killing. The SFWO also anticipates 

that, while some take of the beetle may occur, the long-term results of the proposed management and 

restoration activities will benefit the beetle and its habitat, including the planting of over 50 elderberry 

shrubs during riparian restoration projects. 

Vernal pool crustaceans
266 Stone Lakes NWR Comprehensive Conservation Plan

The SFWO expects that incidental take of the vernal pool tadpole shrimp and vernal pool fairy shrimp 

will be difficult to detect or quantify for the following reasons: the aquatic nature of the organisms 

and their very small body size make the finding of a dead specimen unlikely; losses may be masked 

by seasonal fluctuations in numbers or other causes; and the species occur in habitat that makes them 

difficult to detect. Due to the difficulty in quantifying the number of vernal pool crustaceans that will 

be taken as a result of implementation of the CCP, the SFWO is quantifying take incidental to the 

project as the number of acres of habitat that will be impacted as a result of the action. The SFWO 

anticipates that during the fifteen year life span of the management plan, take of vernal pool crustaceans 

may result from Refuge activities on a maximum of two acres of vernal pools and seasonal swales 

on the North Stone Lake property. However, due to the relatively minimal impacts of the proposed 

activities and the implementation of proposed conservation measures, the SFWO anticipates that 

relatively few vernal pool crustaceans and their cysts within these two acres will be killed, harmed, or 

disturbed by the proposed actions. The SFWO also anticipates that, while some take of vernal pool 

crustaceans will occur, the long-term results of the proposed management and restoration activities will 

benefit vernal pool crustaceans and their habitat.

Effect of the Take

In the accompanying biological opinion, the Service determined that this level of anticipated take is not 

likely to result in jeopardy to the listed wildlife species or destruction or adverse modification of critical 

habitat.

Reasonable and Prudent Measures

The Service believes the following reasonable and prudent measures are necessary and appropriate to 

minimize the impact of take on listed species:

1. Assess over time the effects of management, operations, and maintenance on listed species.

2. Design/ incorporate/ follow measures that reduce or eliminate impacts to listed species.

Terms and Conditions

To be exempt from the prohibitions of section 9 of the Act, the Refuge must comply with the following 

terms and conditions, which implement the reasonable and prudent measures described above. These 

terms and conditions are nondiscretionary.

1. The following term and condition implements reasonable and prudent measure number one 

(Assess the effects of the proposed action on the listed species): 

Develop baseline information for the listed species addressed in this opinion. 

Information shall include, but is not limited to, acreage of occupied and potential habitat 

for each listed species occurring on the Refuge, distribution of habitat, and current status 

of the species. Update the baseline for each listed species when changes occur.

2. The following term and condition implements reasonable and prudent measure number two (Design/ 

incorporate/ follow measures that reduce or eliminate impacts to listed species):

The Refuge shall implement all conservation measures described on pages 13 

through 16 of this biological opinion.

Review Requirements

The reasonable and prudent measures, with their implementing terms and conditions, are designed to 

minimize incidental take that might otherwise result from the proposed action. With implementation 
Stone Lakes NWR Comprehensive Conservation Plan 267

of these measures, the Service believes that incidental take will not exceed for each covered species 

the amount discussed in the previous section - Amount or Extent of Take. If, during the course of the 

action, this minimized level of incidental take is exceeded, such incidental take would represent new 

information requiring review of the reasonable and prudent measures provided. The Refuge must 

immediately provide an explanation of the causes of the taking and review with the Service the need 

for possible modification of the reasonable and prudent measures.

Reporting Requirements

Refuge staff shall forward copies of all research, surveys, or monitoring results on the refuge for listed 

species addressed by this consultation to the SFWO. 

The Sacramento Fish and Wildlife Office is to be notified within three working days of the finding of 

any dead listed wildlife species or any unanticipated harm to the species addressed in this biological 

opinion. The Service contact person for this is the Chief, Endangered Species Division at (916) 414-

6600.

CONSERVATION RECOMMENDATIONS

Section 7(a)(1) of the Act directs Federal agencies to utilize their authorities to further the purposes of 

the Act by carrying out conservation programs for the benefit of endangered and threatened species. 

Conservation recommendations are discretionary agency activities that can be implemented to further 

the purposes of the Act, such as preservation of endangered species habitat, implementation of recovery 

actions, or development of information and data bases.

1. Controlled grazing by goats (Capra hircus) may be used as a method to control the target 

species and thatch on SLNWR particularly within the buffer zones for vernal pools and swales.

2. As recommended in the preliminary draft recovery plan for the giant garter snake, conservation 

measures that could be undertaken by the Refuge include: (1) incorporate giant garter snake 

considerations into Refuge management guidelines, (2) build refugia for giant garter snakes that 

is protected from flooding, (3) expand giant garter snake habitat on the Refuge (Giant Garter 

Snake Recovery Plan, Recovery Task 1.3.5), and (4) conducting periodic surveys on the Refuge 

for the giant garter snake.

3. As recommended in the recovery plan for the valley elderberry longhorn beetle, conservation 

measures that could be undertaken by the Refuge include: (1) conducting periodic surveys 

within the Refuge for the beetle (Recovery Task 2), and (2) removal of exotic trees or shrubs 

such as Chinese tree-of-heaven (Ailanthus altissima), black locust (Robinia pseudoacacia), 

and scotch broom (Cytisus scoparius) that may compete with elderberry (Recovery Task 113). 

Currently tree-of-heaven and scotch broom are not known to occur on the Refuge, however; any 

plants that are discovered in the future should be removed. Other invasive species which may 

be a problem for the beetle and its habitat and should be removed when they are found include 

scarlet wisteria (Sesbania punicea), giant reed (Arundo donax), and pampas grass (Cortaderia 

selloana).

4. For vernal pool crustaceans, restoration of vernal pool habitat within the Refuge is encouraged 

to benefit the vernal pool fairy shrimp and vernal pool tadpole shrimp.

The SFWO requests notification of the implementation of any conservation recommendations.
268 Stone Lakes NWR Comprehensive Conservation Plan

REINITIATION--CLOSING STATEMENT

This concludes formal consultation on the action(s) outlined in your request. As provided in 50 CFR 

§402.16, reinitiation of formal consultation is required where discretionary Federal agency involvement 

or control over the action has been maintained (or is authorized by law) and if: 

(1) the amount or extent of incidental take is exceeded; (2) new information reveals effects of the 

agency action that may affect listed species or critical habitat in a manner or to an extent not considered 

in this opinion; (3) the agency action is subsequently modified in a manner that causes an effect to the 

listed species or critical habitat that was not considered in this opinion; or (4) a new species is listed or 

critical habitat designated that may be affected by the action. In instances where the amount or extent 

of incidental take is exceeded, any operations causing such take must cease pending reinitiation.

Please contact Mary Hammer or Holly Herod of this office at (916) 414-6645 if you have any 

questions. If you have any questions regarding environmental contaminants, contact Tom Maurer at 

(916) 414-6590.

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watersnakes in North America. Final Report to U.S. Fish and Wildlife Service, Sacramento, CA.

Simovich, M., R. Brusca, and J. King. 1992. Invertebrate survey 1991-1993 PGT-PGE/Bechtel 
Stone Lakes NWR Comprehensive Conservation Plan 273

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tadpole shrimp proposed for listing, 1993. Roseville, California. 10 pp. + appendices.

Swanson, G.A., M.I. Meyer, and J.R. Serie. 1974. Feeding ecology of breeding blue-winged teals. J. 

Wildl. Manage. 38(3):396-407.

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in Temporary Ponds of Chaouia Plain (Western Morocco) - Sympatry or Syntopy Between 

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to Congress by the Secretary of the Interior, Washington, D.C., March, 1994. http://www.doi.

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September 19, 1994.

_____ 1999. Draft Giant Garter Snake Recovery Plan. Portland, Oregon.

_____ 1999. Conservation guidelines for the valley elderberry longhorn beetle. Ecological Services 

Office; Sacramento, California. July 9, 1999.
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_____ 2003. Endangered and Threatened Wildlife and Plants; Final Designation of Critical Habitat 

for Four Vernal Pool Crustaceans and Eleven Vernal Pool Plants in California and Southern 

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of the Lower Sacramento Valley and its Effects on the Indigenous Ant Fauna. Hilgardia 55:1-16.

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Imperiled Species in the United States. Bioscience 48 (8): 607-615.

Williams, T. and V. Wunderlich. 2003. Progress report: 2003 San Joaquin Valley giant garter snake 

conservation project. San Luis National Wildlife Refuge Complex, Los Banos, California.

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Area of the San Joaquin Valley. Dixon Field Station, Biological Resources Division, U.S. 

Geological Survey, Dixon, California. 

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Resources Division, U.S. Geological Survey, Dixon, California. 

_____. 2003. Results of the 2003 monitoring for giant garter snakes (Thamnophis gigas): bank 

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108, Sacramento River Bank Protection Project, Phase II. Dixon Field Station, Biological 

Resources Division, U.S. Geological Survey, Dixon, California. 13 pp.

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2001 field season. Dixon Field Station, Biological Resources Division, U.S. Geological Survey, 

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gigas) for the bank protection project on the left bank of the Colusa Basin Drainage Canal 

in Reclamation District 108, Sacramento River Bank Protection Project, Phase II. Prepared 

for: Environmental Planning Section, U.S. Army Corps of Engineers, Sacramento District, 

November 2004.

Wylie, G. D., T. Graham, M. L. Casazza, M. M. Paquin, and J. Daugherty. 1996. National Biological 

Service giant garter snake study progress report for the 1995 field season. Preliminary report. 

Dixon Field Station, Biological Resources Division, U.S. Geological Survey, Dixon, California. 

Wylie, G. D., M. L. Cassaza, and J. K. Daugherty. 1997. 1996 Progress report for the giant garter 

snake study. Preliminary report. Dixon Field Station, Biological Resources Division, U.S. 

Geological Survey, Dixon, California. 
Stone Lakes NWR Comprehensive Conservation Plan 275

Wylie, G. D., M. L. Casazza, L. Martin, and E. Hanson. 2000. Investigations of giant garter snakes in 

the Natomas Basin: 2000 field season. Dixon Field Station, Biological Resources Survey, U.S. 

Geological Survey, Dixon, California. 13 pp.

Wylie, G. D., M. L. Casazza, and N. M. Carpenter. 2002. Monitoring giant garter snakes at Colusa 

National Wildlife Refuge: 2001 progress report. Dixon Field Station, Biological Resources 

Survey, U.S. Geological Survey, Dixon, California. 10 pp.

Wylie, G. D., M. L. Casazza, L. L. Martin, and M. Carpenter. 2003a. Monitoring giant garter snakes 

at Colusa National Wildlife Refuge: 2002 progress report. Dixon Field Station, Biological 

Resources Survey, U.S. Geological Survey, Dixon, California. 16 pp.

Wylie, G. D., M. L. Casazza, and L. L. Martin. 2003b. Giant garter snake surveys in the Natomas 

Basin: 2000-2002. Dixon Field Station, Biological Resources Survey, U.S. Geological Survey, 

Dixon, California. 20 pp.

Wylie, G. D., M. L. Casazza, and M. Carpenter. 2003c. Diet of bullfrogs in relation to predation on 

giant garter snakes at Colusa National Wildlife Refuge. California Fish and Game 89(2): 139-

145.

Wylie, G. D., M. L. Casazza, L. L. Martin, and M. Carpenter. 2004a. Monitoring giant garter snakes 

at Colusa National Wildlife Refuge: 2003 progress report. Dixon Field Station, Biological 

Resources Survey, U.S. Geological Survey, Dixon, California. 17 pp.

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Natomas Basin: 2003 Results. Dixon Field Station, Biological Resources Survey, U.S. 

Geological Survey, Dixon, California. 55 pp.

Personal Communications

Harvey, Tom. Manager, Stone Lakes National Wildlife Refuge 

Nagano, Chris. Deputy Assistant Field Supervisor, Sacramento Field Office
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Appendix G. Response to Public Comments

Once the Draft CCP/EA was complete, a planning update was prepared and mailed out to 379 interested 

stakeholders on September 18, 2006. The planning update announced the availability of the Draft CCP/

EA for review and comment as well as providing notice of the public comment meetings on October 4 and 

5, 2006. On September 25, 2006 a Notice of Availability for the draft CCP/EA published in the Federal 

Register (Vol. 71, No. 185, p. 55801) announcing that the Draft CCP/EA was open to public comment for 

a 30 day period and noting the location and times for public comment meetings. Printed copies of the 

Draft CCP/EA were mailed to 65 interested stakeholders, including local libraries, state agencies, local 

landowners and others and electronic copies were posted for downloading on the Pacific Region Refuge 

Planning website and on the Refuge website.

Due to requests for an extension of the Draft CCP/EA comment period, the public comment period was 

extended for an additional 30 days ending on November 27, 2006. Supplemental notices announcing the 

30 day comment period extension were mailed to 379 interested stakeholders. Many comments were 

received during public meetings and 25 written comments were also received during the comment period.
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1) The comment is acknowledged.

2) There is no formal relationship between the Refuge and the waterskiing club. 

High-speed boating, primarily associated with waterskiing, reportedly has 

occurred on Refuge waterways since before lands and waterways were incorporated 

into the National Wildlife Refuge System as described on page 54 of the CCP/

EA. Compatibility Determinations for existing and proposed visitor uses of the 

Refuge, including high-speed boating, are included as Appendix A of this CCP. 

Compatibility Determinations as described in the National Wildlife Refuge System 

uses compatibility policy (part 603 FW 2), of the U.S. Fish and Wildlife Service 

(Service) Manual, have been completed for high-speed boating on Refuge waters 

and will be used to determine if the described proposed and existing uses are 

determined to be compatible uses of the Refuge. In addition, the appropriate 

refuge uses policy (part 603 FW 1) provides the policy and procedure for refuge 

managers to follow when deciding if uses are appropriate on a refuge. Service 

Manual chapters, can be viewed on the internet at: http://www.fws.gov/policy/

manuals/. 

3) As stated in the National Wildlife Refuge System uses compatibility policy (part 

603 FW 2),” ...the Secretary shall not initiate or permit a new use of a refuge or 

expand, renew, or extend an existing use of a refuge, unless the Secretary has 

determined that the use is a compatible use...” As directed by this policy (part 603 

FW 2), uses found to be incompatible, through a Compatibility Determination, will 

not be allowed on the Refuge whether the use is new or existing. As stated in the 

appropriate refuge uses policy (part 603 FW 1), “...the refuge manager will decide 

if a new or existing use is an appropriate refuge use. If an existing use in not 

appropriate, the refuge manager will eliminate or modify the use as expeditiously 

as practicable.” 

4) The comment is acknowledged.
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5) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determination will be made for 

Refuge uses. 6) The comment is acknowledged. 7) The comment is acknowledged. The direct impact on visitors of noise associated 

with high-speed boating was not included in the draft Compatibility Determination 

for high-speed boating, but has been added to the final version. 8) The comment is acknowledged.
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9) The comment is acknowledged.

10) Thank you for providing the fact sheet.

11) The comment is acknowledged.

12) The comment is acknowledged.
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13) The comment is acknowledged. See response #2 for a description of how 

Compatibility Determinations and Appropriate Use determination will be made for 

Refuge uses.
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14) The comment is acknowledged. Please note that more than 6,000 people 

currently visit the Refuge each year to participate in a variety of wildlife dependent 

recreational and educational activities, as described under Visitor Services 

beginning on page 53 of this CCP. 15) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses. 16) The comment is acknowledged. The direct impact on visitors of noise associated 

with high-speed boating was not included in the draft Compatibility Determination 

for high-speed boating, but has been added to the final Compatibility 

Determination. 

17) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations will be made 

for Refuge uses. 18) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use determinations will be made 

for Refuge uses.
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19) The comment is acknowledged.

20) The comment is acknowledged. The direct impact on visitors of noise associated 

with high-speed boating was not included in the draft Compatibility Determination 

for high-speed boating, but will be added to the final version. 

21) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses. 
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22) The comment is acknowledged.

23) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use determinations will be made 

for Refuge uses.

24) The comment is acknowledged.
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25) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use determinations are made 

for Refuge uses. Please note that all Compatibility Determinations presented in 

the CCP are considered final when the Refuge Compatibility Determination and 

Concurrence have been signed by authorized representatives of the U.S. Fish and 

Wildlife Service. 

26) The comment is acknowledged. Please note that the official Refuge purposes are 

described under the heading “Refuge Purposes” on page 13 of the CCP. 

27) The comment is acknowledged.

28) The comment and personal experience is acknowledged.

29) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use determinations are made for 

Refuge uses. The direct impact on visitors of noise associated with high-speed 

boating was not included in the draft Compatibility Determination for high-speed 

boating, but has been added to the final version.

30) The comment is acknowledged. Please note that the official Refuge purposes are 

described under the heading “Refuge Purposes” on page 13 of the CCP. 

31) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made 

for Refuge uses. Please note that all Compatibility Determinations presented in 

the CCP are considered final when the Refuge Compatibility Determination and 

Concurrence have been signed by authorized representatives of the U.S. Fish and 

Wildlife Service. 
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32) The comment is acknowledged. 

33) The comment is acknowledged. See response # 20.

34) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses.

35) The comment is acknowledged.
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36) The comment is acknowledged.

37) The comment is acknowledged.

38) The comment is acknowledged.
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39) The comment is acknowledged. The U.S. Fish and Wildlife Service’s 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. 40) The comment is acknowledged. 41) The comment is acknowledged. 42) The use of high-speed boats on the Refuge was found to be not appropriate 

through an Appropriateness Determination completed in September of 2006. 

As stated in the Appropriate Refuge Uses policy (part 603 FW 1), “...the refuge 

manager will decide if a new or existing use is an appropriate refuge use. If an 

existing use in not appropriate, the refuge manager will eliminate or modify 

the use as expeditiously as practicable.” However, since the Appropriateness 

Determination policy was finalized on July 26, 2006 a draft Compatibility 

Determination had already been prepared for high speed boating on the Refuge. 

Please note that the Compatibility Determination is considered final when the 

Refuge Compatibility Determination and Concurrence have been signed by 

authorized representatives of the U.S. Fish and Wildlife Service. As stated in the 

National Wildlife Refuge System Uses Compatibility policy (part 603 FW 2),” ...the 

Secretary shall not ...permit...an existing use of a refuge, unless the Secretary 

has determined that the use is a compatible use...” As directed by this policy 

(part 603 FW 2), no uses of the Refuge will be allowed unless the use is found 

to be compatible. Likewise, existing uses found to be not compatible, through a 

Compatibility Determination, will not be allowed on the Refuge. Furthermore 

the Compatibility policy (part 603 FW 2, 2.14) states “Existing uses determined 

to be not compatible will be expeditiously terminated or modified to make the 

use compatible. Except with written authorization by the Director (of the U.S. 

Fish and Wildlife Service), this process of termination or modification will not 

exceed 6 months from the date that the compatibility determination is signed.” 

There is no provision in Refuge System policy to change findings in Compatibility 

Determinations or Appropriateness Determinations on the basis of the Club’s 

financial obligation to a private party. There is no provision in Refuge System 

policy to allow a phase out period in excess of 6 months, for a use found to be not 

compatible, without written authorization by the Director. Therefore it is beyond 

the authority of the Refuge to permit a 7 year phase out period, for high speed 

boating on the Refuge, as recommended in the comment. 

43) We agree with the comment that high speed boating is likely to conflict with 

smaller water craft such as kayaks and canoes. We acknowledge your comment 

regarding the fishing club. 

44) We respectfully disagree with the comment’s assertion that non-motorized 

boating will require facility improvements and increases in staffing and funding. 

Currently basic parking and car-top boat launch facilities exist, on the Beach Lake 

Unit near the end of Elliott Ranch Road, that can accommodate 10-15 vehicles. 

The rationale for Objective 3.B (page 89 of the CCP) states that boating would 

be allowed from June to September, with a no-wake zone in effect for the entire 

Refuge. Non-motorized boats could be launched, by reservation, on the Refuge 

beginning in June 2007, following signature of the final CCP. Please note that 

Objective 3.B also calls for enhancement of boating opportunities, to approximately 

20 cars by 2009; requiring additional facility improvements and increases in 

staffing. 

45) The Refuge will make a reasonable effort to assist the club with finding an 

alternative location for their high speed boating activities. However, the Refuge 

can not guarantee that an alternative location will be found that is acceptable to 

Club members. 

46) Reducing the linear extent of high speed boating associated with waterskiing 

on the Refuge would not eliminate the impacts of high speed boating. Therefore, 
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reducing the scale of high speed boating on the Refuge would not change 

the Compatibility Determination. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses.

47) The CCP does not propose to dedicate any zones exclusively to non-motorized 

watercraft. However, the CCP and EA do propose to restrict all Refuge waters to a 

no-wake zone, to prohibit gasoline powered motor boats, to close waters seasonally 

to all watercraft and to place limitations on the use of electric watercraft motors. 

Reducing the linear extent of high speed boating associated with waterskiing on 

the Refuge would not eliminate the impacts of high speed boating. 

48) The comment is acknowledged. See response # 46.

49) The comment and the estimate of the minimum space needed to facilitate water 

skiing are acknowledged. However, as stated in the National Wildlife Refuge 

System Uses Compatibility policy (part 603 FW 2),” ...the Secretary shall not 

...permit...an existing use of a refuge, unless the Secretary has determined that 

the use is a compatible use...” The Refuge can not allow a use found to be not 

compatible except with written authorization by the Director of the U.S. Fish and 

Wildlife Service (Service Manual, part 603 FW 2, 2.14).

50) The comment is acknowledged.

51) We can not assess the validity of what is meant by “visible levee erosion”. Based 

upon available evidence, we believe that continued high-speed boat traffic on 

the Refuge could lead to the need for extensive levee repair or even levee failure. 

Information in support of the likelihood of high-speed boating impacting levees is 

presented in the Compatibility Determination for high speed boating, beginning on 

page 126, of Appendix A, in the CCP. 

52) The comment is acknowledged.

53) The comment is acknowledged.

54) The comment is acknowledged. See response #45.

55) The comment is acknowledged. See response #42. 

56) The Refuge will make a reasonable effort to assist the club with finding an 

alternative location for their high speed boating activities. However, the Refuge 

can not guarantee that an alternative location will be found that is acceptable to 

ski club members. The Refuge System can not allow the use of refuge resources 

for private economic activities when those uses are found to be not compatible with 

Refuge purposes or not appropriate uses. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses.

57) The CCP proposes many forms of recreation that citizens and families can enjoy 

on the Refuge. Compatibility Determinations conclude the following uses are 

compatible, with stipulations: fishing: wildlife observation and photography; 

environmental education and interpretation; recreational boating associated with 

hunting, fishing, wildlife observation and photography, and plant gathering. Please 

note that the Compatibility Determination are considered final when the Refuge 

Compatibility Determination and Concurrence have been signed by authorized 

representatives of the U.S. Fish and Wildlife Service as described in response #21.
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58) There is no provision in Refuge System policy to allow a phase out period in 

excess of 6 months, for a use found to be not compatible, from the date that a 

Compatibility Determination is signed, without written authorization by the 

Director. Therefore it is beyond the authority of the Refuge to permit a 7 year 

phase out period, for high speed boating on the Refuge, as recommended in the 

comment.

59) See response #46.

60) The Refuge will make a reasonable effort to assist the club with finding an 

alternative location, however the Refuge can not guarantee that an alternative 

location will be found that is acceptable to ski club members. Furthermore, the 

Refuge can not allow a use found to be not compatible to continue except with 

written authorization by the Director of the U.S. Fish and Wildlife Service (Service 

Manual, part 603 FW 2, 2.14) as described in response #49. 
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61) The comment is acknowledged. 
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62) The comment is acknowledged. 63) The comment is acknowledged. 64) The comment is acknowledged. 65) The comment is acknowledged.
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66) The comment is acknowledged. 67) The comment is acknowledged. See response #2 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses. 68) The comment is acknowledged. 69) The Refuge agrees that high-speed boating will likely not be feasible alongside 

non-motorized boats such as canoes and kayaks, as described in draft Compatibility 

Determination for high-speed boating beginning on page 124 of the draft CCP. 70) The comment is acknowledged and we appreciate you sharing your personal 

observations.

71) The comment is acknowledged.
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72) The comment is acknowledged and we appreciate your attendance at the public 

comment meeting in Elk Grove. 73) The comment is acknowledged. 74) The approved Refuge boundary for Stone Lakes National Wildlife Refuge totals 

17,641 acres. The errors are noted and have been changed in the CCP. 75) The comment is acknowledged, and the correct figures have been added to the 

CCP. The entire Refuge consists of 8,740 acres of agriculture, 743 developed acres 

and 8,158 natural areas. These land use types total to 17,641 acres. 76) The core Refuge area consists of 9,146 acres as described on page 7 of the CCP. In the introduction, on page 1, the intent was to describe an approximate acreage 

figure for the core Refuge area. However, for clarity the core Refuge figure on page 

1 will be corrected to 9,146 acres. 77) The cooperative wildlife management area totals 9,066 acres. In the introduction, 

on page 1, the intent was to describe an approximate acreage figure for the 

cooperative wildlife management area. However, for clarity the cooperative wildlife 

management area figure on page 1 will be corrected to 9,066 acres. 78) While both of the actively managed acre figures are approximate estimates, the 

figure on page 1 and 8 (6,200 acres actively managed) is more accurate. The figures 

on page 109 and 174 (6,000 acres) have been changed to the more accurate estimate 

of 6,200 acres. 

79) The figure on page 8 (6,200 acres actively managed) is the most accurate 

estimate. The figure on page 216 in the Fire Management Plan (4,000 acres 

actively managed) was considered an accurate estimate in 2001, when the Fire 

Management Plan was written. When the Fire Management Plan is updated in 

the future, the figure of actively managed acres will be updated as well. 

80) The precise acreage owned in fee title is 1,746.9 acres. The figure for acreage 

owned in fee title on page 8 (1,740 acres owned in fee title) was intended as an 

approximate figure and was preceded by the word “about” to indicate that the 

figure was an estimate. The figure on page 8 has been corrected to 1,746.9 acres 

for clarity. The figure on page 313 of the “Wilderness Review” (2,000 discontinuous 

acres) is inaccurate and has been corrected and clarified. 
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81) The acres under conservation easements total 1,533.56. The acres under 

cooperative agreements total 1,567.00. The approximate estimate on page 8 has 

been corrected to reflect these, more accurate figures. The figure on page 216 in 

the Fire Management Plan (over 2,700 acres under cooperative agreement) was 

considered an accurate estimate of lands managed under cooperative agreements 

and easements in 2001, when the Fire Management Plan was written. When 

the Fire Management Plan is updated in the future, the figure of cooperatively 

managed acres and easement acres will be updated. 

82) The general terms of easements and cooperative agreements that the Refuge 

will enter into are described under “Land Conservation Methods” and “Related 

Projects and Studies in the Area” on page 8 and 13 respectively of the CCP. The 

CCP describes the preferred alternative, which is consistent with the terms of all 

easements entered into or that would be entered into by the Refuge within the 

approved Refuge boundary. In addition, all individual easements and agreements 

are publicly-recorded documents that are available from the Refuge headquarters 

upon request. 

83) Objective 1.H and the associated strategies describe how non-irrigated grasslands 

will be managed and enhanced on the North Stone Lake Unit. The CCP does not 

propose expansion of grasslands on the Refuge. The 30 acres planted to restore 

the native grassland community, described in the environmental assessment 

(alternatives table on page 190 of the CCP), will result in conversion of primarily 

non-native grasslands to primarily native grasslands and does not describe 

expansion of overall grassland acreage. 

84) Lands described on page 8 as private lands and lands “managed for conservation 

purposes by five local and State agencies” are not all managed by the Refuge under 

cooperative agreements. However, lands owned by Sacramento County Parks 

(1,567 acres) and Caltrans (150 acres) are managed by the Refuge. Copies of 

these management agreements are available from the Refuge headquarters upon 

request. Lands owned by the California State Parks (1,073 acres), the California 

Department of Water Resources (410 acres) and the Sacramento Regional County 

Sanitation District (1,800 acres) are not managed by the Refuge, but may still be 

managed, by local and State agencies, for conservation purposes as indicated on 

page 8 of the CCP. 

85) There is no requirement to provide a summary of environmental documentation 

for all prior actions on a Refuge in a CCP. The “History of Refuge Establishment 

and Acquisition” section summaries previous land conservation efforts on the 

Refuge. Specific inquiries regarding other previous actions should be referred to 

the Refuge and are beyond the scope of the CCP.

86) The comment is acknowledged. See response #82.

87) The cooperative agreement with Sacramento County Department of Regional 

Parks, Recreation and Open Space was finalized in 1999 and relates to joint 

management of grassland habitat on the North Stone Lake Unit and is consistent 

with the habitat restoration and management goals and objectives of the CCP. 

88) The draft cooperative agreement is included for illustrative purposes only. See 

response #82 for a description of why actual cooperative agreements have not 

been included with the CCP. There are no changes to the Fire Management Plan 

proposed as part of the CCP process, although it will be updated outside of the CCP 

process in the future. The Fire Management plan is included in the appendices for 

informational purpose only.

89) A summary of the Draft North Stone Lake Management and Restoration Plan 

is provided on page 14 of the CCP. The proposed action to manage the Refuge 

according to the goals, objectives and strategies described beginning on page 73 

of the CCP is consistent with the Draft North Stone Lakes Management and 

Restoration Plan. 
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90) No County policies will become Federal policies. 91) The environmental assessment, Appendix B of the CCP, applies only to the 

current proposed action described in the CCP. Refuge land conservation 

efforts such as cooperative agreements are provided for under the 1992 Final 

Environmental Impact Statement, establishing the approved Refuge boundary 

(USFWS 1992). The Refuge determined that re-establishing a livestock grazing 

program on the North Stone Lake Unit was an acceptable habitat management 

approach and not a significant Federal action necessitating individual NEPA 

documentation. Please contact the Refuge for more information on prior actions, 

not addressed in this CCP.

92) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use determinations will be made for Refuge uses. The section (5.F.) 

of the draft 1998 cooperative agreement (Appendix C.4) that you evidently refer to 

relates to Sacramento County not permitting hunting on their North Stone Lake 

property. The Refuge hunting program occurs in the South Stone Lake Unit on 

land owned in fee title by the Service and is consistent with policies of the National 

Wildlife Refuge System. For more informaion on refuge hunting, please refer to the 

Stone Lakes Waterfowl Hunting Plan, available on the internet at : http://www.fws.

gov/stonelakes/Waterfowl%20Hunt%20Plan.pdf

93) The Service must obtain concurrence from Sacramento County Department 

of Water Resources that any earthwork proposed by the Service for the countyowned portion of the North Stone Lake property will not affect floodplain storage. 

Objectives and strategies for management of refuge floodplain lands are described 

on page 84 of the CCP. 

94) The comment is acknowledged. The section referred to was completed in 2001 

and is included for informational purposes only. 

95) By definition, lands under joint management must be administered in a manner 

consistent with the goals of the cooperating parties signatory to the agreement. 

The Service has determined that the North Stone Lake Unit can be cooperatively 

managed consistent with the CCP and contribute to the mission of the National 

Wildlife Refuge System. 
316 Stone Lakes NWR Comprehensive Conservation Plan
Stone Lakes NWR Comprehensive Conservation Plan 317

96) See response #82 for an explanation regarding inclusion of specific easements and 

agreements as part of the CCP. 

97) Page 14, of the CCP, describes the total SRCSD property as 2,650 acres only 1,800 

of which lie within the approved Refuge boundary. The Fire Management Plan, 

describes the North Stone Lakes Unit as being 2,700 acres in size which includes 

the treatment plant and the surrounding 2,650 acres of “buffer lands”. There is 

no contradiction in these acreage figures, but the reader should consider the figure 

of 2,650 as lands the Refuge would be interested in managing to fulfill Refuge 

purposes. 

98) See response #82 for an explanation regarding inclusion of specific easements 

and agreements as part of the CCP. The precise acreage under a conservation 

easement is 1,533.56. The precise acreage under cooperative agreement is 

1,567.00. The approximate estimate on page 8 has been corrected to reflect these 

more accurate figures. 

99) The comment is acknowledged. The sentence has been edited to reflect accurate 

mileage.

100) The comment is acknowledged and the figure will be corrected to the current 

figure available from the Cosumnes River Preserve. The current total acreage of 

the Cosumnes River Preserve, at the time of CCP completion, was 46,000 acres 

(Jaymee Marty, pers. comm. Cosumnes River Preserve Biologist). 

101) See response #82 for a description of the management that will be applied to 

lands within the Refuge under the proposed action. The manner in which Refuge 

lands have been conserved by the Service are illustrated in Figures 2, 3, and 4.

102) We agree that a landowner or management agency can be a discharger. On 

page 34 of the draft CCP the paragraph refers to adjacent irrigated lands that are 

not owned or managed by the Refuge. The paragraph has been clarified in the final 

CCP. The section referred to is under an introductory review of Refuge Resources 

and is not intended to be a definitive statement on discharged water quality laws, 

regulations or policies. Detailed questions about local water quality regulations 

should be referred to the Central Valley Regional Water Quality Control Board.

103) Given the limited resources available for preparation of the CCP, the Service 

believes it has adequately characterized issues related to water quality and 

agricultural drainage within the approved Refuge boundary. 

104) The comment is acknowledged.
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Stone Lakes NWR Comprehensive Conservation Plan 319

105) The comment is acknowledged. At this time the Service believes that the 

management of Refuge lands and waters described in the CCP is consistent with 

State water law, Refuge purposes, the National Wildlife Refuge System mission, 

and Service policies. 

106) The comment is acknowledged. Given limited resources for plan 

development, the CCP can only describe the water resources necessary to achieve 

the action detailed in the CCP and does not seek to quantify all water sources, 

rights, and management actions.

107) Within the framework of the CCP an objective is a concise statement of what 

and how much is to be achieved, where it will occur and who is responsible for its 

completion. Objectives derive from goals and provide the basis for determining 

strategies. Strategies are a specific action, tool, technique, or combination of 

actions, tools, and techniques to meet unit objectives. Objectives and strategies 

are worded as specifically as possible. Any follow-up actions lacking sufficient 

detail in the CCP and associated NEPA document may require a separate analysis 

of potential impacts for compliance with the National Environmental Policy Act, 

the Endangered Species Act and other applicable laws and regulations.

108) Strategy 1.K.6. addresses a cooperative agreement with Sacramento 

Regional County Sanitation District for joint management of the Bufferlands 

surrounding the Regional Wastewater Treatment Plant. Finalization of this 

agreement would not necessitate additional NEPA documentation since the 

resulting inter-agency coordination and habitat management would not constitute 

a major new Federal action and would be consistent with the CCP. 

109) Finalization of an agreement with California Department of Parks and 

Recreation would not necessitate additional NEPA documentation since the 

resulting enhanced inter-agency coordination and habitat management would not 

constitute a major new Federal action and would be consistent with the CCP.

110) See response #82 for an explanation regarding inclusion of specific 

easements and agreements as part of the CCP.

111) See response #109.

112) See response #109.

113) Preparation of a cooperative agreement with California Department of 

Water Resources for joint management of their 410 acres within the approved 

Refuge boundary (Strategy 1.L.3) would not necessitate additional NEPA 

documentation since the resulting inter-agency coordination and habitat 

management would not constitute a major new Federal action and would be 

consistent with the CCP. 

114) The joint operating agreement for the Cosumnes River Preserve is the 

overall agreement defining the roles and responsibilities of the private and 

public cooperators participating in the Preserve. Addressing the cumulative 

environmental effects of this agreement was the responsibility of the signatories. 

115) The comment is acknowledged.

116) The Morrisson Creek dam is actually a levee which is maintained by the 

City and County of Sacramento and does not currently lie within the Refuge. The 

City and County do no operate the levee other than passively allowing it to be 

overtopped as water surface elevations to the north or south increase. We believe 

that the environmental assessment (Appendix B) provides sufficient information to 

evaluate the effects of current and proposed Refuge water management practices 

on the environment as described under “Water Quantity and Quality” on page 208 

of this CCP. 

117) See response to #116. 

118) Operational details of water control structures affecting the Refuge 

including gates and dams are discussed: under “Water Supply” beginning on page 

37; under “Wetlands” beginning on page 58; and under “Basin Hydrology and 
320 Stone Lakes NWR Comprehensive Conservation Plan
Stone Lakes NWR Comprehensive Conservation Plan 321

Water Quality” beginning on page 66. 

119) The comment is acknowledged.

120) The comment is acknowledged. 

121) The Service believes there is adequate description of the policies and actions 

proposed by the CCP to satisfy NEPA requirements. 
322 Stone Lakes NWR Comprehensive Conservation Plan
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122) The comment is acknowledged. 123) The comment is acknowledged. Any cooperating fire management agency or 

agencies will be clarified in future agreements. 124) The comment is acknowledged. 125) The comment is acknowledged. The Service believes there is sufficient 

background information provided in the CCP regarding existing and proposed 

agreements. 126) As defined in the National Wildlife Refuge System Improvement Act of 1997, 

the terms “ ‘purposes of the refuge’ and ‘purposes of each refuge’ mean the purposes 

specified in or derived from the law...establishing, authorizing, or expanding a 

refuge, refuge unit, or refuge subunit.” The purpose(s) of a refuge unit do not 

change over time. We respectfully disagree with the statement that the “Refuge 

purposes and goals...were extended ...over the years.” The goals presented in the 

CCP and associated NEPA document are unique to the CCP. Prior management 

agreements were in accord with the Environmental Impact Statement finalized in 

1992, prior to Refuge establishment in 1994. 127) The comment is acknowledged. 128) There is no proposal in the CCP to control waterskiing on the Refuge. 

See response #2 for a discussion of compatible and appropriate uses of Refuge 

lands, including waterskiing associated with high speed boating. There is wellestablished legal precedent under the Endangered Species Act of 1973 (16 U.S.C. 

1531-1544, 87 Stat. 884) and the Migratory Bird Treaty Act of 1918 (16 U.S.C. 703-

712; Ch. 128; July 13, 1918; 40 Stat. 755) as amended for the Service to regulate 

boating on navigable and non-navigable waters of the U.S. when these waterways 

are under the ownership of the Service.

129) The comment is acknowledged. The Service has adequately determined the 

extent of property boundaries to be able to administer visitor activities on lands 

and waters within the Refuge. 

130) The comment is acknowledged. Deer do not occur on the Refuge in sufficient 

numbers to warrant consideration of a deer hunting program.

131) The comment is acknowledged.

132) See response #130. 

133) The comment is acknowledged.

134) The comment is acknowledged.

135) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses.

136) We respectfully disagree. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use determinations are made for 

Refuge uses.

137) The comment is acknowledged.

138) The comment is acknowledged. 
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139) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses. Grazing has been 

found to be a compatible use with stipulations in the Compatibility Determination 

for grazing on the Refuge, which is included in Appendix A. As stated in the 

Compatibility Determination's justification, the goals for grazing on the Refuge 

are to conserve, enhance, restore and manage Central Valley wetland, riparian, 

grassland and other native habitats to benefit their associated fish, wildlife, plants 

and special status species. 140) The comment is acknowledged; however see response #3 for a description 

of how Compatibility Determinations and Appropriate Use Determination will be 

made for Refuge uses. 141) We respectfully disagree. The Service has found no evidence to suggest 

that there would be any significant impacts to the environment from the proposed 

action. 

142) Any future projects or actions lacking sufficient detail in the CCP and 

associated NEPA document will receive separate analyses of potential impacts in 

compliance with the National Environmental Policy Act, the Endangered Species 

Act and other applicable laws, policies, and regulations. 

143) There is no Alternative D in the Environmental Assessment for the CCP.

144) See response #3 for a description of how Compatibility Determinations 

and Appropriate Use Determinations are made for Refuge uses. Lands managed 

as part of the National Wildlife Refuge System are managed to fulfill the Refuge 

purpose(s), the mission of the National Wildlife Refuge System and Service 

policies. Policies for the management of National wildlife refuges may or may not 

coincide with the management policies for other federal lands. The Service does not 

prescribe to a formulaic acreage-based approach to determine the extent of public 

trails on a refuge unit.

145) There is no Alternative D in the environmental assessment for the CCP.

146) There is no Alternative D in the environmental assessment for the CCP.
326 Stone Lakes NWR Comprehensive Conservation Plan
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147) The comment is acknowledged.

148) The comment is acknowledged.
328 Stone Lakes NWR Comprehensive Conservation Plan
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149) The comment is acknowledged.

150) The comment is acknowledged.

151) The comment is acknowledged. However, please note that the Compatibility 

Determination will be considered final when the Refuge Compatibility 

Determination and Concurrence have been signed by authorized representatives of 

the U.S. Fish and Wildlife Service. 

152) The Refuge has attempted to include sufficient detail related to wildlife 

and habitat management in this CCP such that a step down habitat management 

plan may not be necessary. In the event that more site or species-specific planning 

becomes necessary and as more staffing and resources become available, the 

Refuge will consider preparation of further step-down plans. We agree with the 

comment's suggestion that fisheries, wildlife, and habitat management are interrelated and the Refuge will consider integrating these plans.
330 Stone Lakes NWR Comprehensive Conservation Plan
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153) The comment is acknowledged.

154) The comment is acknowledged.

155) The comment is acknowledged.
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156) The comment is acknowledged.

157) Construction of picnic areas has not been considered on the Refuge due, in 

part, to limited Refuge staff for the maintenance of picnic facilities. Picnicking 

is also not identified as a priority wildlife-dependent use in the National Wildlife 

Refuge Improvement Act of 1997. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses.
338 Stone Lakes NWR Comprehensive Conservation Plan
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158) The comment is acknowledged. 

159) The sentence will be corrected to the turn of the 20th century, for 

clarification.

160) The Refuge agrees that it would be desirable to monitor for Perchlorate, 

NDMA, TCE and other constituents, however additional staff and project funds 

will be required to implement such a monitoring program. 

161) The comment is acknowledged. With the staff resources available, the 

Refuge seeks and will continue to seek opportunities to work with partners, 

including those mentioned to fulfill the Refuge purpose, to fulfill the mission of the 

National Wildlife Refuge System and to comply with Service policies. 

162) The comment is acknowledged. Obtaining and providing the data requested 

would be an unreasonable burden in the completion of the CCP and could only 

be obtained with great cost, particularly given the need for complex modeling to 

estimate highly variable stream flows and hydrology. 

163) The comment is acknowledged. Obtaining and providing complete water 

rights information for areas around the Refuge would be an unreasonable burden 

in the completion of the CCP and could only be obtained with great cost.

164) See response #162.

165) See response #162.

166) See response #162.

167) The comment is acknowledged. 

168) Generating the data requested regarding mitigation would be an 

unreasonable burden in the completion of the CCP and could only be obtained at 

great cost.

169) The comment is acknowledged, but we disagree with the suggestion. Within 

Refuge staff and monitoring resources, the ground water monitoring described is 

not considered feasible. The Refuge’s highest priorities are to fulfill the Refuge 

purpose and to fulfill the mission of the National Wildlife Refuge System.

170) The comment is acknowledged, however given limited project funds the 

Refuge’s highest priorities are to fulfill the Refuge purpose and to fulfill the 

mission of the National Wildlife Refuge System.

171) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses.

172) The comment is acknowledged.

173) The comment is acknowledged

174) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations will be made for Refuge uses.

175) The comment is acknowledged.

176) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses.

177) We disagree that strategy 1.G.1. is inconsistent with Goal 3. We believe 

visitors can be provided with wildlife recreation, interpretation, and education 

opportunities which foster an understanding of the Refuge’s unique wildlife and 

plant communities in an urban setting (Goal 3) while at the same time reducing 

wildlife disturbance by limiting access to certain locations (strategy 1.G.1.).

178) The comment is acknowledged. Please note that the Refuge supports an 

adaptive management approach.
340 Stone Lakes NWR Comprehensive Conservation Plan
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179) The target of 10,500 visit opportunities per year is not a limit, but rather a 

target number of opportunities to offer to the public. 180) The term visit opportunities can be defined as “An opportunity for a member 

of the public to visit the Refuge for a staff guided or self-guided wildlife-dependent 

recreation or other event.” This definition has been added to the glossary. 181) The comment is acknowledged. See response #3. 182) The comment is acknowledged. See response #3. 183) There is no prescription in the draft CCP for boating only with undefined 

trolling motors. Please see the Compatibility Determination for Recreational 

Boating, in Appendix A, for a full discussion of boating, other than high-speed 

boating, on the Refuge. 184) It is not clear how the comment defines boating trails. See response #3 

for a description of how Compatibility Determinations and Appropriate Use 

Determinations are made for Refuge uses. 185) The comment is acknowledged. See response #3. 186) The comment is acknowledged. It is not clear from the comment which 

sections are considered by the author to be partly intertwined and confusing. 187) We disagree that the CCP or Compatibility Determinations misconstrue 

impacts. The Compatibility Determinations reflect the sound professional 

judgment of the Refuge Manager.

188) We disagree that vegetation is a barrier to access, particularly along 

roadways where vegetation is regularly mowed. Proposed car top boating access on 

the Refuge would only occur at specific improved access sites and therefore would 

have no incremental or cumulative impacts.

189) Given currently available staff and project funds, we disagree that bank 

fishing requires less staff effort, based largely on the need for regular trash 

removal and public safety associated with bank fishing on the Refuge. Please note 

that a step-down fisheries management plan is proposed for completion in 2008, 

which will address management of fishing on the Refuge, possibly including bank 

fishing.

190) We disagree, and the comment offers no evidence to support this statement.

191) The comment is acknowledged but it is unclear what if any opportunities 

are being removed. While boating may require special skills and access to boats, 

it is not clear how this would remove opportunities from others without boats and 

special skills as suggested in this comment.

192) The comment is acknowledged.

193) The comment is acknowledged. See response # 189.

194) The Compatibility Determination for wildlife observation and photography 

describes facilities and materials to support the level of uses as described in the 

CCP, which would require additional project funds and staff.

195) The Compatibility Determination for wildlife observation and photography 

found that the use is compatible with stipulations, as can be seen in Appendix 

A. See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses.

196) The comment is acknowledged. Improvements to the railroad right-of-way 

would be at the discretion of the landowner, since the alignment does not currently 

lie within the Refuge. With available resources the Refuge’s highest priorities 

are to fulfill the Refuge purpose and to fulfill the mission of the National Wildlife 

Refuge System.

197) The comment is acknowledged, but we disagree with your conclusion. The 

author does not offer any evidence to contradict findings in the cited reference. 

198) We agree and content related to environmentally-friendly recreation already 

is and will continue to be a part of the educational programs proposed for the 

Refuge in the CCP. 
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199) The comment is acknowledged.

200) The comment is acknowledged.

201) The comment is acknowledged.

202) The comment is acknowledged.

203) The comment is acknowledged and a correction has been made.
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204) The statement regarding the California tiger salamander was intended as 

a general statement and should not be interpreted as applying to the Refuge since 

there have been no documented sightings of California tiger salamander on the 

Refuge. The statement has been clarified.
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205) The comment is acknowledged. 206) The comment is acknowledged. See response #42. 207) The comment is acknowledged. 208) The comment is acknowledged. See response #42. 209) According to the Beach Lake Ski Club (see response #41), the Club is “...

financially obligated to a 10-year contractual lease agreement with Mr. Harvey 

Collins for access purposes...expiring year end 2013.” If this statement, from the 

Beach Lake Ski Club, is accurate then the author would have in excess of 7 years to 

find alternative uses for the property described. In addition, the Refuge is bound to 

follow federal policies for allowing use on Refuge lands and waterways as described 

in response #3. 
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210) The comment is acknowledged. See response #3.

211) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations will be made for Refuge uses. Grazing has been 

found to be a compatible use, with stipulations, in the Compatibility Determination 

for grazing on the Refuge, found in Appendix A. As stated in the Compatibility 

Determination justification, the goals for grazing on the Refuge are to conserve, 

enhance, restore, and manage Central Valley wetland, riparian, grassland and 

other native habitats to benefit their associated fish, wildlife, plants, and special 

status species. 

212) The comment is acknowledged. See response #195.

213) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses.
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214) See response #42. 215) The comment is acknowledged. 216) The comment is acknowledged, however we are not aware of the study 

referenced by the comment’s author, nor was the citation offered. See response 

#3 for a description of how Compatibility Determinations and Appropriate Use 

Determinations are made for Refuge uses.
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217) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses.
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218) The comment is acknowledged.

219) The comment is acknowledged.

220) The comment is acknowledged.
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221) The comment is acknowledged. 222) The Refuge recognizes that wetlands may contribute to biomagnifications 

of methylmercury through the food web. What is known about methylmercury 

and other contaminants on the Refuge is summarized under “Contaminants 

and Water Quality” beginning on page 32 of the CCP. Objective 1.N., beginning 

on page 85 of the CCP, specifies that the Refuge will monitor for mercury and 

other contaminants and work toward achieving the water quality standard for 

wetlands and fish and wildlife resources set forth by the USEPA, the DFG and 

the Regional Water Quality Control Board. Furthermore, as stated on page 210 

of the environmental assessment " Refuge staff will continue to comply with 

National Pollution Discharge Elimination System general permit protocols and 

best management practices for aquatic herbicide applications and water quality 

monitoring that were developed by the Central Valley Regional Water Quality 

Control Board to avoid adverse effects on water quality and aquatic wildlife." 223) The comment is acknowledged. 224) The comment is acknowledged. We believe that nothing in the CCP is 

inconsistent with the draft Basin Plan. No actions proposed in the CCP should be 

interpreted to suggest violation of the water quality supply standard for wetlands 

and fish and wildlife resources set forth by the USEPA, the DFG or the Regional 

Water Quality Control Board. For additional information, please contact Refuge 

staff.
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225) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses.

226) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations are made for Refuge uses. The Compatibility 

Determination for recreational boating on the Refuge, contained in Appendix A, 

found that recreational boating was compatible with stipulations.

227) Please see some actions related to your suggestions under Goal 4 and the 

related objectives, beginning on page 92 of this CCP. While there is no plan to 

construct a village on the Refuge, the CCP does propose to work with the Ione 

Band of Miwok Indians or with other involved tribal organizations to meet some of 

the educational goals that the author suggests.
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228) The comment is acknowledged. The U.S. Fish and Wildlife Service’s 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." We always 

appreciate hearing from those outside of the Service.
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229) The comment is acknowledged. The current Refuge waterfowl hunting 

program offers the greatest number of hunting blinds to the general public and 

secondarily to youth and disabled hunters. 

230) The comment is acknowledged. 

231) The comment is acknowledged. 
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232) The comment is acknowledged. Figure 5 has been corrected in this CCP.

233) The text has been changed to reflect the current situation.

234) The text has beem clarified for strategy 1.H.6.

235) The comment is acknowledged. Please note that strategy 1.J.4. calls for 

using local expertise in developing native grassland restoration plans. When 

restoration plans are finalized, it is possible that native forbs and other components 

of native grasslands will be included as a part of the restoration plan. However, 

resources for restoration are limited and while the complete restoration of native 

grassland habitats including native forbs is desirable, it may not be possible within 

the life of the CCP given limited resources available for grassland restoration. 
366 Stone Lakes NWR Comprehensive Conservation Plan
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236) The comment is acknowledged.

237) The comment is acknowledged.

238) The comment is acknowledged. Please see response #229 for a discussion of 

current hunt opportunities on the Refuge.

239) See response #3 for a description of how Compatibility Determinations and 

Appropriate Use Determinations will be made for Refuge uses.

240) The comment is acknowledged. There is well-established legal precedent 

under the Endangered Species Act of 1973 (16 U.S.C. 1531-1544, 87 Stat. 884) and 

the Migratory Bird Treaty Act of 1918 (16 U.S.C. 703-712; Ch. 128; July 13, 1918; 

40 Stat. 755) as amended for the Service to regulate boating on navigable and nonnavigable waters of the U.S. when these waterways are under the ownership of the 

Service.

241) The comment is acknowledged.
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242) The comment is acknowledged, however we disagree. In the sound 

professional judgment of the Refuge manager there is not enough land owned in fee 

title to provide a safe and quality upland game hunting experience on the Refuge. 

243) The comment is acknowledged.

244) The comment is acknowledged.

245) The comment is acknowledged.

246) The comment is acknowledged. Many strategies associated with objectives 

under Goal 1 detail the proposed enhancements of wetland and associated upland 

habitats.

247) Mosquito control on the Refuge was found to be a compatible use in the 

Compatibility Determination, contained in Appendix A, of this CCP with the 

stipulations listed. 

248) The comment is acknowledged.
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249) The comment is acknowledged.

250) The comment is acknowledged. See response #3 for a description of how 

Compatibility Determinations and Appropriate Use Determinations are made for 

Refuge uses.

251) The comment is acknowledged. The Service has and will continue to 

abide by commitments made as part of the 1992 Final Environmental Impact 

Statement (EIS) and subsequent Record of Decision establishing the Stone Lakes 

NWR approved boundary. For example as cited on page FJ-52, of the 1992 Final 

EIS, the Service will establish adequate internal buffers “...whenever sensitive 

wildlife habitat areas are developed adjacent to any farmlands other than range or 

pasture.”

252) As we have previously communicated, Refuge staff are willing to assist the 

author and other interested landowners to secure an “incidental taking plan” (i.e., 

Safe Harbor Agreement) that addresses routine land management operations on 

nearby privately-owned properties.
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253) The comment is acknowledged, and the text has been updated.

254) The comment is acknowledged, and the text has been updated.
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255) The comment is acknowledged, and the text has been updated.

256) The comment is acknowledged, and the text has been updated.

257) The comment is acknowledged, and the text has been updated.

258) The comment is acknowledged, and the text has been updated.
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259) The comment is acknowledged, and the text has been updated.

260) The comment is acknowledged, and the text has been updated.
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261) The comment is acknowledged, and the text will be updated. 
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Appendix H. Plant Species Found on Stone Lakes 

National Wildlife Refuge

Stone Lakes NWR Plants

Scientific name Common 

name U.S. nativity Duration Growth habit Group

ACERACEAE (maple family)

Acer negundo var. 

californicum

box elder native perennial tree dicot

ALISMATACEAE (water plantain family)

Alisma lanceolatum water plantain introduced perennial forb/herb monocot

Echinodorus berteroi burhead native perennial forb/herb monocot

Sagittaria latifolia arrowhead native perennial forb/herb monocot

ANACARDIACEAE (sumac family)

Toxicodendron 

diversilobum

poison oak native perennial shrub/vine monocot

APIACEAE (carrot family)

Daucus carota wild carrot introduced biennial forb/herb dicot

Foeniculum vulgare fennel introduced biennial, 

perennial

forb/herb dicot

Scandix pecten-veneris Venus’ needle introduced annual forb/herb dicot

APOCYNACEAE (dogbane family)

Apocynum cannabinum indian hemp native perennial forb/herb dicot

ASCLEPIADACEAE (milkweed family)

Asclepias fascicularis narrow leaf 

milkweed

native perennial forb/herb dicot

Asclepias incarnata milkweed native perennial forb/herb dicot

ASTERACEAE (aster family)

Achyrachaena mollis blow-wives native perennial forb/herb dicot

Acroptilon repens russian 

knapweed

introduced perennial forb/herb dicot

Ambrosia psilostachya western 

ragweed

native perennial forb/herb dicot

Anthemis cotula chamomile introduced annual forb/herb dicot

Artemisia douglasiana mugwort native perennial forb/herb dicot

Aster subulatus var.

ligulatus

southern 

annual 

saltmarsh 

aster

native annual, 

biennial

forb/herb dicot

Baccharis pilularis coyote bush native perennial subshrub, 

shrub

dicot

Bidens frondosa nodding 

beggarticks

native annual forb/herb dicot
382 Stone Lakes NWR Comprehensive Conservation Plan

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Carduus pycnocephalus italian thistle introduced annual forb/herb dicot

Centaurea solstitialis yellow star 

thistle

introduced annual forb/herb dicot

Matricaria discoidea (syn.

Chamomilla suaveolens)

pineapple 

weed

introduced annual forb/herb dicot

Cichorium intybus chicory introduced biennial, 

perennial

forb/herb dicot

Cirsium vulgare bull thistle introduced biennial forb/herb dicot

Conyza canadensis horseweed native annual, 

biennial

forb/herb dicot

Coreopsis wrightii tickseed native annual forb/herb dicot

Euthamia occidentalis grass-leaved 

goldenrod

native perennial forb/herb dicot

Gnaphalium luteo-album cudweed, 

weedy

introduced annual forb/herb dicot

Gnaphalium palustre cudweed, 

everlasting

native annual forb/herb dicot

Gnaphalium stramineum cudweed, 

everlasting

native annual, 

biennial

forb/herb dicot

Grindelia camporum gum plant native perennial subshrub, 

forb/herb

dicot

Helianthus annuus sunflower native annual forb/herb dicot

Hemizonia fitchii fitch’s tarweed native annual forb/herb dicot

Centromadia pungens 

(syn. Hemizonia pungens)

spikeweed native annual forb/herb dicot

Hesperevax caulescens dwarf dwarfcudweed

native annual forb/herb dicot

Heterotheca grandiflora telegraph 

plant

native annual, 

biennial, 

perennial

forb/herb dicot

Holocarpha virgata holocarpha native annual forb/herb dicot

Hypochaeris glabra smooth cats 

ear

introduced annual forb/herb dicot

Hypochaeris radicata rough cat’s-ear introduced perennial forb/herb dicot

Lactuca serriola prickly lettuce introduced annual, 

biennial

forb/herb dicot

Lasthenia californica California 

goldfields

native annual, 

perennial

forb/herb dicot

Lasthenia fremontii Fremont’s 

goldfields

native annual forb/herb dicot

Lasthenia glaberrima smooth 

goldfields

native annual forb/herb dicot

Layia chrysanthemoides tidy tips native annual forb/herb dicot

Madia elegans ssp.

vernalis

common madia native annual forb/herb dicot
Stone Lakes NWR Comprehensive Conservation Plan 383

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Picris echioides bristly oxtongue

introduced annual forb/herb dicot

Psilocarphus brevissimus wooly heads native annual forb/herb dicot

Psilocarphus oregonus Oregon woolyheads

native annual forb/herb dicot

Senecio vulgaris common 

groundsel

introduced annual, 

biennial

forb/herb dicot

Silybum marianum milk thistle introduced annual, 

biennial

forb/herb dicot

Sonchus asper ssp. asper prickly sow 

thistle

introduced annual forb/herb dicot

Sonchus oleraceus annual 

sowthistle

introduced annual forb/herb dicot

Xanthium spinosum spiny 

cocklebur

introduced annual forb/herb dicot

Xanthium strumarium cocklebur native annual forb/herb dicot

BORAGINACEAE (borage family)

Amsinckia menziesii var. 

intermedia

fiddleneck native annual forb/herb dicot

Heliotropium 

curassavicum

heliotrope native annual, 

perennial

subshrub, 

forb/herb

dicot

Plagiobothrys greenei popcorn flower native annual forb/herb dicot

Plagiobothrys leptocladus alkali popcorn 

flower

native annual forb/herb dicot

Plagiobothrys stipitatus 

var. micranthus

stalked 

popcornflower

native annual forb/herb dicot

Plagiobothrys stipitatus 

var. stipitatus

stalked 

popcornflower

native annual forb/herb dicot

Plagiobothrys 

trachycarpus

roughfruit 

popcornflower

native annual forb/herb dicot

BRASSICACEAE (mustard family)

Brassica nigra black mustard introduced annual forb/herb dicot

Brassica rapa field mustard introduced annual, 

biennial

forb/herb dicot

Capsella bursa-pastoris shepherd’s 

purse

introduced annual forb/herb dicot

Cardamine oligosperma little western 

bittercress

native annual, 

biennnial, 

perennial

forb/herb dicot

Cardaria chalepensis lens-podded 

hoary-cress

introduced perennial shrub dicot

Lepidium latifolium perennial 

peppergrass

introduced perennial forb/herb dicot

Lepidium latipes var.

heckardii

Heckard’s 

peppergrass

native annual forb/herb dicot
384 Stone Lakes NWR Comprehensive Conservation Plan

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Lepidium nitidum var.

nitidum

shining 

pepperweed

native annual forb/herb dicot

Raphanus raphanistrum jointed 

charlock

introduced annual, 

biennial

forb/herb dicot

Raphanus sativus wild radish introduced annual, 

biennial

forb/herb dicot

Rorippa curvisiliqua yellow cress native annual, 

biennial

forb/herb dicot

CALLITRICHACEAE (water-starwort family)

Callitriche trochlearis water starwort native annual forb/herb dicot

CAMPANULACEAE (bellflower family)

Downingia bicornuta var.

bicornuta

downingia native annual forb/herb dicot

Downingia ornatissima 

var. ornatissima

folded 

calicoflower

native annual forb/herb dicot

Legenere limosa legenere native annual forb/herb dicot

CAPRIFOLIACEAE (honeysuckle family)

Sambucus nigra (syn. 

Sambucus mexicana)

elderberry native perennial shrub, tree dicot

Symphoricarpos albus var.

laevigatus

snowberry native perennial subshrub, 

shrub

dicot

CARYOPHYLLACEAE (pink family)

Cerastium glomeratum sticky 

chickweed

introduced annual forb/herb dicot

Silene gallica catchfly introduced annual, 

biennial

forb/herb dicot

Spergula arvensis ssp.

arvensis

starwort introduced annual forb/herb dicot

Spergularia bocconii sand-spurry introduced annual forb/herb dicot

Stellaria media common 

chickweed

introduced annual forb/herb dicot

CHENOPODIACEAE (goosefoot family)

Chenopodium album lamb’s 

quarters

native, 

introduced

annual forb/herb dicot

Chenopodium 

ambrosioides

Mexican tea introduced annual, 

perennial

forb/herb, 

subshrub

dicot

Chenopodium multifidum chenopodium introduced annual forb/herb dicot

Salsola tragus russian 

tumbleweed

introduced annual forb/herb dicot

CONVOVULACEAE (morning-glory family)

Convolvulus arvensis bindweed introduced perennial vine, forb/

herb

dicot
Stone Lakes NWR Comprehensive Conservation Plan 385

Scientific name Common 

name U.S. nativity Duration Growth habit Group

CRASSULACEAE (stonecrop family)

Crassula aquatica water 

pygmyweed

native annual forb/herb dicot

CUCURBITACEAE (cucumber family)

Marah fabaceus manroot native perennial vine, forb/

herb

dicot

CUSCUTACEAE (dodder family)

Cuscuta pentagona dodder native annual, 

perennial

vine, forb/

herb

dicot

CYPERACEAE (sedge family)

Carex praegracilis carex native perennial graminoid monocot

Cyperus eragrostis sedge native perennial graminoid monocot

Cyperus erythrorhizos redroot 

flatsedge

native annual, 

perennial

graminoid monocot

Cyperus esculentus yellow nut 

sedge

native, 

introduced

perennial graminoid monocot

Eleocharis macrostachya spike rush native perennial graminoid monocot

Schoenoplectus acutus 

(syn. Scirpus acutus var. 

occidentalis)

hardstem 

bulrush

native perennial graminoid monocot

Schoenoplectus 

mucronatus (syn. Scirpus 

mucronatus)

bog bulrush introduced perennial graminoid monocot

Scirpus robustus alkali bull rush native perennial graminoid monocot

Schoenoplectus glaucus 

(syn. Scirpus tuberosus)

scirpus introduced perennial graminoid monocot

EUPHORBIACEAE (spurge family)

Chamaesyce maculata spotted 

sandmat

native annual forb/herb dicot

Eremocarpus setigerus turkey mullin, 

doveweed

native annual forb/herb dicot

FABACEAE (pea family)

Glycyrrhiza lepidota wild licorice native perennial forb/herb dicot

Lotus corniculatus trefoil introduced perennial forb/herb dicot

Lotus unifoliolatus 

var. unifoliolatus (syn. 

Lotus purshianus var. 

purshianus)

lotus native annual forb/herb dicot

Lupinus albifrons var. 

albifrons

lupine native perennial subshrub, 

shrub

dicot

Lupinus bicolor annual lupine native annual forb/herb dicot

Medicago polymorpha California 

burclover

introduced annual, 

perennial

forb/herb dicot
386 Stone Lakes NWR Comprehensive Conservation Plan

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Medicago sativa alfalfa introduced annual, 

perennial

forb/herb dicot

Melilotus alba white 

sweetclover

introduced annual, 

biennnial, 

perennial

forb/herb dicot

Melilotus indica yellow 

sweetclover

introduced annual forb/herb dicot

Trifolium depauperatum 

var. depauperatum

balloon clover native annual forb/herb dicot

Trifolium dubium hopclover, 

shamrock

introduced annual forb/herb dicot

Trifolium fucatum bull clover native annual forb/herb dicot

Trifolium hirtum rose clover introduced annual forb/herb dicot

Trifolium microdon thimble clover native annual forb/herb dicot

Trifolium variegatum whitetip clover native annual forb/herb dicot

Trifolium willdenovii tomcat clover native annual forb/herb dicot

Vicia sativa ssp. nigra common vetch introduced annual vine, forb/

herb

dicot

Vicia villosa hairy vetch introduced annual, 

biennnial, 

perennial

vine, forb/

herb

dicot

FAGACEAE (beech family)

Quercus douglasii blue oak native perennial tree dicot

Quercus lobata valley oak native perennial tree dicot

Quercus wislizenii live oak native perennial tree dicot

Centaurium 

muehlenbergii

centaury native annual, 

biennial

forb/herb dicot

Erodium botrys broad leaf 

cranes bill

introduced annual, 

biennial

forb/herb dicot

Erodium cicutarium red stemmed 

filaree

introduced annual, 

biennial

forb/herb dicot

Erodium moschatum whitestemmed 

filaree

introduced annual, 

biennial

forb/herb dicot

GERANIACEAE (geranium family)

Geranium carolinianum Carolina 

geranium

native annual, 

biennial

forb/herb dicot

Geranium dissectum geranium introduced annual, 

biennial

forb/herb dicot

HYDROPHYLLACEAE (waterleaf family)

Nemophila menziesii baby blue-eyes native annual forb/herb dicot

Nemophila pedunculata nemophila native annual forb/herb dicot
Stone Lakes NWR Comprehensive Conservation Plan 387

Scientific name Common 

name U.S. nativity Duration Growth habit Group

IRIDACEAE (iris family)

Sisyrinchium bellum blue-eyed 

grass

native perennial forb/herb monocot

JUGLANDACEAE (walnut family)

Juglans californica var. 

hindsii

black walnut native perennial tree dicot

JUNCACEAE (rush family)

Juncus arcticus ssp.

littoralis (syn. Juncus 

balticus)

baltic rush native perennial graminoid monocot

Juncus bufonius toad rush native annual graminoid monocot

Juncus patens rush native perennial forb/herb monocot

Juncus phaeocephalus rush native perennial graminoid monocot

Juncus xiphioides irisleaf rush native perennial graminoid monocot

LAMIACEAE (mint family)

Lamium amplexicaule henbit introduced annual, 

biennial

forb/herb dicot

Lycopus americanus bugleweed native perennial forb/herb dicot

Marrubium vulgare white 

horehound

introduced perennial subshrub, 

forb/herb

dicot

Mentha pulegium pennyroyal introduced perennial forb/herb dicot

Pogogyne douglasii Douglas’ 

mesamint

native annual forb/herb dicot

Pogogyne ziziphoroides Sacramento 

mesamint

native annual forb/herb dicot

Stachys ajugoides hedge nettle native perennial forb/herb dicot

Trichostema lanceolatum vinegar weed native annual forb/herb dicot

LAURACEAE (laurel family)

Umbellularia californica California bay 

tree

native perennial tree, shrub dicot

LILIACEAE (lily family)

Asparagus officinalis ssp.

officinalis

asparagus introduced perennial forb/herb monocot

Brodiaea elegans ssp. 

elegans

harvest 

brodiaea

native perennial forb/herb monocot

Chlorogalum 

pomeridianum

soap root native perennial forb/herb monocot

Dichelostemma capitatum 

ssp. capitatum

blue dicks native perennial forb/herb monocot

Triteleia hyacinthina white brodiaea native perennial forb/herb monocot

Triteleia laxa Ithuriel’s 

spear

native perennial forb/herb monocot
388 Stone Lakes NWR Comprehensive Conservation Plan

Scientific name Common 

name U.S. nativity Duration Growth habit Group

LYTHRACEAE (loosestrife family)

Ammannia coccinea ammannia native annual forb/herb, 

subshrub

dicot

Lythrum hyssopifolia hyssop 

loosestrife

introduced annual, 

biennial

forb/herb dicot

Lythrum tribracteatum threebract 

loosestrife

introduced perennial forb/herb dicot

MALVACEAE (mallow family)

Abutilon theophrasti velvetleaf introduced annual forb/herb dicot

Malva neglecta cheeses introduced annual, 

biennnial, 

perennial

forb/herb dicot

Malvella leprosa alkali mallow native perennial forb/herb dicot

OLEACEAE (olive family)

Fraxinus latifolia Oregon ash native perennial tree dicot

ONAGRACEAE (evening primrose family)

Epilobium brachycarpum willowweed native annual forb/herb dicot

Epilobium canum zauschneria native perennial subshrub, 

forb/herb

dicot

Epilobium ciliatum willow weed native perennial forb/herb dicot

Epilobium pygmaeum epilobium native annual forb/herb dicot

Ludwigia peploides ssp.

peploides 

water 

primrose

native perennial forb/herb dicot

PAPAVERACEAE (poppy family)

Eschscholzia californica California 

poppy

native annual, 

perennial

forb/herb dicot

PLANTAGINACEAE (plantain family)

Plantago coronopus buckhorn 

plantain

introduced annual, 

biennial

forb/herb dicot

Plantago elongata little plantain native annual forb/herb dicot

Plantago lanceolata English 

plantain

introduced annual, 

biennnial, 

perennial

forb/herb dicot

PLATANACEAE (plane-tree family) 

Platanus racemosa California 

sycamore

native perennial tree dicot

POACEAE (grass family)

Alopecurus saccatus foxtail native annual graminoid monocot

Avena fatua wild oats introduced annual graminoid monocot

Briza minor quaking grass introduced annual graminoid monocot

Bromus carinatus California 

brome

native annual, 

perennial

graminoid monocot

Bromus diandrus ripgut brome introduced annual, 

perennial

graminoid monocot
Stone Lakes NWR Comprehensive Conservation Plan 389

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Bromus hordeaceus soft chess introduced annual graminoid monocot

Bromus madritensis ssp.

rubens

foxtail chess introduced annual graminoid monocot

Crypsis schoenoides swamp grass introduced annual graminoid monocot

Crypsis vaginiflora swamp 

timothy

introduced annual graminoid monocot

Cynodon dactylon bermuda grass introduced perennial graminoid monocot

Deschampsia cespitosa tufted 

hairgrass

native perennial graminoid monocot

Distichlis spicata salt grass native perennial graminoid monocot

Echinochloa crus-galli water grass introduced annual graminoid monocot

Elymus glaucus blue wild rye native perennial graminoid monocot

Elymus trachycaulus wheat grass native perennial graminoid monocot

Eragrostis mexicana Mexican 

lovegrass

native annual graminoid monocot

Schedonorus phoenix (syn.

Festuca arundinacea)

tall fescue introduced perennial graminoid monocot

Festuca brevipila (syn.

Festuca trachyphylla)

hard fescue introduced perennial graminoid monocot

Hordeum 

brachyantherum

meadow 

barley

native perennial graminoid monocot

Hordeum jubatum foxtail barley native perennial graminoid monocot

Hordeum marinum ssp.

gussonianum

mediterranean 

barley

introduced annual graminoid monocot

Hordeum murinum ssp.

leporinum

foxtail barley introduced annual graminoid monocot

Koeleria macrantha junegrass native perennial graminoid monocot

Leymus triticoides creeping wild 

rye

native perennial graminoid monocot

Leptochloa uninervia Mexican 

sprangletop

native annual, 

perennial

graminoid monocot

Lolium perenne ssp.

multiflorum (syn. Lolium 

multiflorum)

annual rye 

grass

introduced annual, 

perennial

graminoid monocot

Melica californica California 

melic

native perennial graminoid monocot

Muhlenbergia rigens deer grass native perennial graminoid monocot

Nassella cernua nodding 

needlegrass

native perennial graminoid monocot

Nassella pulchra purple needle 

grass

native perennial graminoid monocot

Paspalum dilatatum dallis grass introduced perennial graminoid monocot

Phalaris californica California 

canarygrass

native perennial graminoid monocot
390 Stone Lakes NWR Comprehensive Conservation Plan

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Phalaris minor canary grass introduced annual graminoid monocot

Phalaris paradoxa hood 

canarygrass

introduced annual graminoid monocot

Phleum pratense cultivated 

timothy

introduced perennial graminoid monocot

Poa annua annual 

bluegrass

introduced annual graminoid monocot

Poa bulbosa bulbous 

bluegrass

introduced perennial graminoid monocot

Polypogon monspeliensis rabbit foot 

grass

introduced annual graminoid monocot

Setaria pumila bristly foxtail introduced annual graminoid monocot

Sorghum halepense johnsongrass introduced perennial graminoid monocot

Taeniatherum caputmedusae

medusahead introduced annual graminoid monocot

Vulpia myuros rat tail fescue introduced annual graminoid monocot

POLYGONACEAE (buckwheat family)

Polygonum amphibium 

var. emersum

water 

smartweed

native perennial forb/herb dicot

Polygonum arenastrum common 

knotweed

introduced annual, 

perennial

forb/herb dicot

Polygonum lapathifolium willow 

smartweed

native annual forb/herb dicot

Polygonum persicaria thumbprint 

smartweed

probably 

introduced

annual, 

perennial

forb/herb dicot

Polygonum punctatum annual 

smartweed

native annual, 

perennial

forb/herb dicot

Rumex conglomeratus clustered dock introduced perennial forb/herb dicot

Rumex crispus curly dock introduced perennial forb/herb dicot

Rumex maritimus golden dock native annual, 

biennial

forb/herb dicot

Rumex pulcher fiddle dock introduced perennial forb/herb dicot

POLEMONIACEAE (phlox family)

Linanthus montanus mustang 

clover

native annual forb/herb dicot

Navarretia leucocephala whitehead 

navarretia

native annual forb/herb dicot

PONTEDERIACEAE (water-hyacinth family)

Eichhornia crassipes water hyacinth introduced perennial forb/herb dicot

PORTULACEAE (purslane family)

Calandrinia ciliata red maids native annual forb/herb dicot

Claytonia parviflora miners lettuce native annual forb/herb dicot

Claytonia perfoliata ssp. 

mexicana

miners’ lettuce native annual forb/herb dicot
Stone Lakes NWR Comprehensive Conservation Plan 391

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Montia fontana water 

chickweed

native annual forb/herb dicot

PRIMULACEAE (primrose family) 

Anagallis arvensis scarlet 

pimpernel

introduced annual, 

biennial

forb/herb dicot

RANUNCULACEAE (buttercup family) 

Clematis ligusticifolia virgin’s bower native perennial vine dicot

Ranunculus bonariensis 

var. trisepalus

buttercup native annual forb/herb dicot

Ranunculus muricatus spiny-fruited 

buttercup

introduced annual, 

biennnial, 

perennial

forb/herb dicot

Rosa californica California rose native perennial subshrub dicot

Rubus armeniacus (syn.

Rubus discolor)

himalayan 

blackberry

introduced perennial subshrub dicot

Rubus ursinus California 

blackberry

native perennial subshrub dicot

RUBIACEAE (madder family)

Cephalanthus occidentalis 

var. californicus

California 

button willow

native perennial tree, shrub dicot

Galium tricornutum rough corn 

bedstraw

introduced annual forb/herb dicot

SALICACEAE (willow family)

Populus fremontii Fremont’s 

cottonwood

native perennial tree dicot

Salix exigua sandbar willow native perennial tree, shrub dicot

Salix gooddingii Goodding’s 

willow

native perennial tree dicot

Salix laevigata red willow native perennial shrub dicot

Salix lasiolepis arroyo willow native perennial tree, shrub dicot

Salix lucida ssp.

lasiandra

yellow willow native perennial tree, shrub dicot

SCROPHULARIACEAE (figwort family) 

Castilleja attenuata valley tassels native annual forb/herb dicot

Castilleja campestris ssp.

campestris

owl’s clover native annual forb/herb dicot

Castilleja campestris ssp.

succulenta

succulent owl’s 

clover

native annual forb/herb dicot

Castilleja exserta purple owl’s 

clover

native annual forb/herb dicot

Kickxia spuria sharppoint 

fluellin

introduced annual forb/herb dicot

Diplacus aurantiacus 

ssp. aurantiacus (syn. 

Mimulus aurantiacus)

orange bush 

monkeyflower

native perennial subshrub, 

shrub

dicot
392 Stone Lakes NWR Comprehensive Conservation Plan

Scientific name Common 

name U.S. nativity Duration Growth habit Group

Mimulus glaucescens 

(syn. Mimulus guttatus)

shieldbract 

monkeyflower

native annual forb/herb dicot

Mimulus latidens broadtooth 

monkeyflower

native annual forb/herb dicot

Mimulus tricolor tricolor 

monkeyflower

native annual forb/herb dicot

Triphysaria eriantha ssp.

eriantha

ohnny jumpupnative annual forb/herb dicot

Triphysaria pusilla dwarf owl’sclover

native annual forb/herb dicot

Veronica peregrina ssp.

xalapensis

purslane 

speedwell

native annual forb/herb dicot

Veronica persica persian 

speedwell

introduced annual forb/herb dicot

SOLANACEAE (potato family)

Nicotiana quadrivalvis coyote tobacco native annual forb/herb dicot

Physalis lanceolata ground cherry native perennial forb/herb dicot

TYPHACEAE (cat-tail family)

Typha angustifolia cattail introduced perennial forb/herb monocot

Typha latifolia narrow leaf 

cattail

native perennial forb/herb monocot

Urticaceae (nettle family)

Urtica dioica stinging 

nettles

native and 

introduced

perennial forb/herb dicot

Urtica urens dwarf nettle introduced annual forb/herb dicot

Phyla nodiflora phyla native perennial forb/herb dicot

Verbenaceae (Verbena family) 

Verbena bonariensis verbena introduced annual, 

biennnial, 

perennial

subshrub, 

forb/herb

dicot

Viscaceae (Christmas mistletoe family)

Phoradendron 

macrophyllum ssp.

macrophyllum

(syn. Phoradendron 

tomentosum ssp.

macrophyllum)

mistletoe native perennial subshrub, 

shrub

dicot

Vitaceae (grape family)

Vitis californica wild grape native perennial vine dicot

Zygophyllaceae (Creosote-bush family)

Tribulus terrestris puncturevine introduced annual forb/herb dicot

All plant scientific names confirmed by: USDA, NRCS. 2006. The PLANTS Database (http://plants.

usda.gov, August 2006). National Plant Data Center, Baton Rouge, LA 70874-4490 USA. 

 
Stone Lakes NWR Comprehensive Conservation Plan 393

Appendix I. Glossary

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. 

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. 

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. 

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

where surface water does not flow out. 

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. 

Carnivore. An animal that kills and eats other animals. 
394 Stone Lakes NWR Comprehensive Conservation Plan

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. 

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). 

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). 

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

another. 

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, 
Stone Lakes NWR Comprehensive Conservation Plan 395

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. 

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). 

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. 

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 

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

especially those of non-literate peoples. 

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. 

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). 
396 Stone Lakes NWR Comprehensive Conservation Plan

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. 

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

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. 

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

and reproduction. The place where an organism typically lives. 

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.). 

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. 

Lethal Dose 50 (LD50). The LD50 or colloquially, semi-lethal dose of a particular substance 

is a measure of how much constitutes a lethal dose. The related units of an LD50/30 or 

an LD50/60 are used to refer to a dose that without treatment will be lethal to 50% of the 

population within (respectively) 30 or 60 days.

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. 

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. 
Stone Lakes NWR Comprehensive Conservation Plan 397

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.” 

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. 

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

NEPA. National Environmental Policy Act of 1969. 

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

continued. 

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. 

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. 

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. 
398 Stone Lakes NWR Comprehensive Conservation Plan

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. 

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 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 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. 

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

Refuge. Short of National Wildlife Refuge. 

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). 

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

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

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

Sound Professional Judgment. 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. 

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

that can interbreed and produce young. A category of biological classification. 
Stone Lakes NWR Comprehensive Conservation Plan 399

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). 

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. 

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

an extended basis. Uplands are non-wetland areas. 

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. 

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. 

Visit Opportunity. An opportunity for a member of the public to visit the Refuge for a staff 

guided or self-guided wildlife-dependent recreation or other event

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

Anseriformes). 

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

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. 

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). 

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

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 
400 Stone Lakes NWR Comprehensive Conservation Plan

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

public uses always will take precedence. 
Stone Lakes NWR Comprehensive Conservation Plan 401

Appendix J. Summary of Public Involvement/

Comments and Consultation/

Coordination

The initial public scoping process for this CCP is described in Chapter 2, The Planning 

Process. 

Once the Draft CCP/EA was complete, a planning update was prepared and mailed 

out to interested stakeholders on September 18, 2006. The planning update 

announced the availability of the Draft CCP/EA for review and comment as well 

as providing notice of the public comment meetings on October 4 and 5, 2006. On 

September 25, 2006 a Notice of Availability for the draft CCP/EA published in the 

Federal Register (Vol. 71, No. 185, p. 55801) announcing that the Draft CCP/EA 

was open to public comment for a 30 day period and noting the location and times 

for public comment meetings. Printed copies of the Draft CCP/EA were mailed to 

interested stakeholders, including local libraries, and electronic copies were posted for 

downloading on the Pacific Region Refuge Planning website and on the Stone Lakes 

NWR website.

Due to requests for an extension of the Draft CCP/EA comment period from the public 

and an elected official, the public comment period was extended for an additional 30 

days ending on November 27, 2006. Supplemental notices announcing the 30 day 

comment period extension were mailed to interested stakeholders.

Responses to written comments on the Draft CCP/EA can be found in Appendix G, 

Response to Comments.

A summary of public comments from the Stone Lakes NWR Draft CCP/EA public 

meetings held on October 4 & 5, 2006 follows. Public comments received during the 

public comment period represented a sub-set of the overall written comments received 

during the open comment period. Appendix G displays responses to all of the written 

comments received and those respondes are incorporated into this Appendix by 

reference. 

Public comments noted during public comment meetings on 10/4/06

Biological Resources Management Comments

•	 Because of good management in some areas, species such as sand hill 

cranes, ravens and other birds are back in the area, but these are away 

from areas of human disturbance such as water skiing. 

•	 (I) expect that other wildlife such as turtles, otter, beaver, nesting herons 

would return to SP cut (if high speed boating ceased). 

•	 Stone Lakes NWR is for the birds.

Visitor Services Comments

•	 In order to maintain biological integrity and fulfill biological goals in 

the preferred alternative, there should be no high speed boating on any 

portion of the Refuge.

•	 Supports banning of high-speed boating because of deleterious effects on 
402 Stone Lakes NWR Comprehensive Conservation Plan

wildlife.

•	 Refuge does not have other inappropriate uses such as OHV (off highway 

vehicles) use, rifle ranges, model planes or jet skis. 

•	 (Want) more fishing access, non-boat pier (access).

•	 Any public access on Southern Pacific Rail Road should ensure no trespass/

vandalism occurs

•	 (Want) increased opportunities for visitor use. (Should) allow bank fishing.

•	 High speed boating should continue on all or a portion of refuge 

waterways.

•	 Motor boats cause noise pollution as well as oil and air pollution.

•	 High speed boating in the SP cut constitutes an exclusive use and prevents 

other uses.

•	 Levee berm erosion has occurred (in the SP cut) and the only wave action 

in the channel is from high speed boating since there is no east wind.

General Comments

•	 Supports the preferred alternative.

•	 (Should) put cooperative agreements in (the) conservation plan.

•	 Should have a more detailed description of the planning process.

•	 Should clarify how comments on NEPA document and CDs will be 

addressed.

•	 A 60 day comment period would be more appropriate than a 30 day 

comment period (the document is long and difficult to read through in 30 

days).

•	 Questioned designation of SP cut as navigable waters since the 

throughway was created by dredging.

•	 Environmental health should be a priority (ex. water quality, vector 

control).

•	 Environmental health should not be at the bottom of the pyramid (figure 

used in power point presentation by Refuge Planner). (He is) concerned 

about vector control and environmental health. 

Public comments noted during public comment meetings on 10/5/06

Biological Resources Management Comments

•	 Sand hill cranes need a large amount of space and are very sensitive to 

noise disturbance.

•	 Sand hill cranes tend to go to the same area every year regardless of the 

crop type there.

•	 There is (poor) bad roosting in agricultural areas, (whereas) wetlands 

allow good roosting. 

•	 Sand hill cranes eat corn, wheat, California voles and may start at tomato 

fields. It is unknown why they start at the tomato fields, but it may be 

related to the alkali soils in those areas.

Visitor Services Comments

•	 Concern was expressed about water skiing on the Refuge. (The person 

commenting) feels that it (water skiing) is not compatible and is disruptive 

to wildlife. Water skiing is noisy, polluting (gas, fumes, noise) and is 

unhealthy for wildlife.

•	 (The person commenting) thinks that kayaks & canoes are o.k. since they 

provide people with another way to see the Refuge and they are less noisy 
Stone Lakes NWR Comprehensive Conservation Plan 403

and slower moving, which allows wildlife to escape. 

•	 It is not a good experience to kayak in the SP cut with high speed boats 

passing at speeds of 15-45 mph.

•	 (The person commenting) has seen water skiers scare away wildlife and 

almost hit an otter. Also wildlife refuge visitors who were observing 

wildlife were disrupted by the water skiers.

•	 (The water skiing use) is inconsistent because the skiers use is 

uncontrolled. The Refuge would control the numbers of canoes and 

kayakers to ensure quality of their visit. We do not know when or who 

comes and goes with the water skiers.

•	 (The Refuge) is also a Refuge for city dwellers to think, be quiet and 

contemplate. (Visitors) should not come to the Refuge and encounter more 

noise (such as boat engines). Areas with quiet places are becoming rarer.

•	 (The person commenting would like to see) removal of skiing because of 

wake erosion, particularly on the west side. (The person commenting) has 

seen (negative) effects on native vegetation such as oaks. In many cases 

(the) water-side berm has been completely eroded away.

•	 Today (a visitor) can see many trees that used to be anchored on the bank 

(that) are now in the water.

•	 Waves created by high-speed boats (are the) primary cause of erosion. 

Erosion is worse on the west side where (the) levee is and (there are) 

cattails, etc. on (the) east side that may dissipate waves. (The) SP cut 

run(s) north to south, so winds do not come directly from east to west. 

Therefore winds are not the cause of (levee) erosion.

•	 The addition of paddle tours on the Refuge would be a good addition, to 

educate (the) public and provide wildlife viewing opportunities. But, in 

the narrow channel of (the) SP cut, canoeing and kayaking would not be 

compatible with high speed boating, which could swamp boats and would 

flush all of the wildlife. 

•	 (The person commenting) has experience with personal (high speed) 

watercraft disrupting (the) experience of paddlers.

•	 In order to encourage canoes and kayakers, (the Refuge) would need to 

eliminate high speed boating.

•	 (The compatibility determinations) should explore all non-motorized types 

of watercraft.

•	 Any non-motorized craft should be allowed.

•	 Paddling is like having a trail in the water.

General Comments

•	 (The Refuge) should increase outreach to groups. ECOS is a local 

umbrella organization that should be contacted.

•	 (The Refuge) should add Yolo Audubon to the mailing list. 
404 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 405

Appendix K. Preparer List

David Bergendorf: National Wildlife Refuge Planner, CA/NV Refuge Planning Office 

Jeanne Clark: Writer/Editor, Private Consultant 

Clay Courtright: Former Wildlife Biologist, Stone Lakes National Wildlife Refuge 

Miki Fujitsubo: Former National Wildlife Refuge Planner, CA/NV Refuge Planning Office 

Thomas Harvey: Project Leader, Stone Lakes National Wildlife Refuge 

Amy Hopperstad: Volunteer Coordinator, Stone Lakes National Wildlife Refuge 

Leslie Lew: Former National Wildlife Refuge Planner, CA/NV Refuge Planning Office

Laurie Litman: Writer/Editor, Private Consultant 

Alex Morton: National Wildlife Refuge Planner, CA/NV Refuge Planning Office 

Mark Pelz: Chief of National Wildlife Refuge Planning, CA/NV Refuge Planning Office 

Beatrix Treiterer: Assistant Refuge Manager, Stone Lakes National Wildlife Refuge 
406 Stone Lakes NWR Comprehensive Conservation Plan

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Stone Lakes NWR Comprehensive Conservation Plan 407

Appendix L. Integrated Pest Management Plan for 

Mosquito-Associated Threats

Integrated Pest Management Plan for Mosquito-Associated Threats

Stone Lakes National Wildlife Refuge

August, 2006

I. Introduction

Stone Lakes National Wildlife Refuge (Refuge) collaborates with the Sacramento-Yolo 

Mosquito Vector Control District (District) in monitoring and controlling mosquitoes to 

ensure the human health concerns of neighboring communities are addressed. The Refuge is 

located within Sacramento County, 10 miles south of downtown Sacramento and bordered by 

the city of Elk Grove on the east. The potential for mosquitoes to be produced or harbored 

on the Refuge is a concern to nearby residents and urbanized areas immediately adjacent 

to the Refuge are well within the flying range of many species of mosquitoes. Because of 

this and commitments made by the U.S. Fish and Wildlife Service (Service) in the Final 

Environmental Impact Statement (1992) establishing the Refuge approved boundary, the 

Service entered into a Memorandum of Understanding (MOU) in 1993, to ensure the public 

health and well-being of residents would not be adversely affected by mosquitoes from the 

Refuge. This Integrated Pest Management (IPM) Plan for Mosquito and Associated Threats 

will facilitate implementation of the MOU and ensure mosquito management practices are 

consistent with Service IPM policies and regulations regarding management of the national 

wildlife refuge (NWR) system. 

Refuge Description

Stone Lakes National Wildlife Refuge was established in 1994 becoming the 505th NWR. 

The approved Refuge boundary encompasses 17,640 acres, of which approximately 6,200 

acres are currently managed by the Service. Stone Lakes NWR lies between the Coast 

and Diablo Ranges to the west and the Sierra Nevada to the east. Most of the Refuge lies 

within the 100-year floodplain of the Mokelumne and Cosumnes rivers. Interstate highway 

5 roughly bisects the Refuge north to south. Annual temperature in the area averages 

approximately 61.0 F degrees and annual precipitation averages approximately 17.93 inches; 

virtually all of the precipitation occurs during the winter months. Summer is typically hot 

(>100 °F) and dry; winter temperatures are generally moderate (50-60 °F). Habitats on the 

Refuge consist of upland grasslands (55 percent), riparian forest and associated shrublands 

(7 percent), open water (7%), seasonal and permanent wetlands including vernal pools 

and irrigated pastures (26 percent), and croplands (5 percent). Land uses adjacent to the 

Refuge include farming (vineyards, orchards and row crops), grazing, and suburban housing 

developments.

Memorandum of Understanding (MOU)

The 1993 MOU between the District and the Refuge outlines a mosquito management 

program that includes consultation on wetland design and water management, use of 

physical, biological and chemical control agents to control mosquito larvae and adults, and 

cooperative research on landbird populations. Both the Refuge and the District agree that 
408 Stone Lakes NWR Comprehensive Conservation Plan

biological, cultural and physical control methods are preferred over chemical measures 

and that wetlands can be designed and managed to minimize mosquito production. In 

summary, the MOU provides for: 1) allowing the District to review planned Refuge wetland 

construction projects; 2) providing the District an annual summary of the upcoming Refuge 

water management program and notification of flood ups and irrigations; 3) the District 

providing a proposed annual mosquito abatement operating plan to the Refuge, 4) the 

Refuge submitting pesticide use proposals (PUP’s), as needed, for any chemical mosquito 

control agents requested by the District; 5) providing access to the District for mosquito 

monitoring and control as defined in an annual Special Use Permit (SUP); and 6) with 

notification and coordination, application of larvicides or adulticides by the District, when 

treatment thresholds are exceeded.

II. Mosquito Borne Disease

Disease History

Due partly to its climate, California has a history of serious arboviral disease problems 

that are not expected to diminish. Western equine (WEE) and St. Louis encephalitis 

(SLE) viruses are endemic and intermittently represent significant public health threats 

throughout the state. St. Louis encephalitis, historically a rural disease in the western 

USA, has now moved into the expanding metropolitan areas of southern California. Several 

international arboviral diseases have recently been introduced to the United States, such 

as dengue, Venezuelan equine encephalitis, and West Nile virus (WNV). 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 also cause diseases in horses 

and emus, and WNV kills a wide variety of endemic and imported birds. Mosquito control is 

practically the only known method of protecting people and animals from WEE, SLE, and 

WNV. With the exception of available vaccines to protect horses against WEE and WNV, 

there are no known specific treatments or cures for the diseases caused by these viruses (CA 

Dept. of Health Services 2004). 

West Nile virus was introduced into New York City during 1999 and has subsequently 

expanded its occurrence dramatically throughout North America. It was first documented 

as becoming established in California in 2004 when a total of 822 human cases were verified, 

primarily in southern California (Table 1). Of the 58 counties in the state, 23 reported virus 

activity during 2004, based on a range of monitoring methods, including: mosquito pools, 

sentinel chicken flocks, wild birds, or equine and human cases (CA Dept. of Heath Services 

2004, CA West Nile Virus website 2006). During 2005, 54 counties were documented as 

supporting virus activity as it moved northward into the Central Valley and the northern 

state. In 2005, Sacramento County was recognized as a focus of WNV activity in the state. 

Table 1. West Nile virus human cases in California (2004-2006). Numbers in parentheses 

are totals for Sacramento and Yolo counties.

Year Human Cases Human Fatalities

2004 822 25

(4) (0)

2005 935 19

(189) (1)

2006 

(as of 08/18/06)

50 1

(16) (0)

A number of characteristics of the Sacramento region may have contributed to this, 
Stone Lakes NWR Comprehensive Conservation Plan 409

including: (1) number of days per year temperatures exceed 95 degrees Fahrenheit., (2) 

abundance of mosquito production habitat particularly rice fields, irrigated pasture, dairies, 

and wetlands, (3) abundance of local migratory bird populations, (4) burgeoning human 

population interfacing with nearby agricultural lands, (5) heavy spring rains, and (6) the 

relative abundance of the primary WNV vector, Culex tarsalis (P. Sanders, SYMVCD, pers.

comm.). During 2004-2005, human cases were documented in the state from approximately 

the first week of July through the first week of November. To date, there have been 16 

human WNV cases in Sacramento and Yolo counties and one mortality in Butte County. 

WNV activity has been detected in a total of 43 counties. The five major species of birds 

most commonly found dead and testing positive for WNV in the state have been American 

crow, Western scrub-jay, yellow-billed magpie, American robin, and house finch. 

A statewide encephalitis virus surveillance program has been in place since the 1960s 

that tracks mosquito abundance and enzootic transmission (transmission within the same 

geographic area) to provide an early warning of the potential for human infection. WEE and 

SLE have been recorded in the Central Valley since the 1940s reappearing intermittently 

after periods of apparent extinction. Though SLE has been rare since 1972, WEE enzootic 

transmission in the Sacramento Valley appears to be cyclic, recurring at 10 year intervals 

(Reisen et al. 1995). WEE is transmitted enzootically during the summer between wild 

birds and Culex tarsalis, while Ocheloratus melanimon is involved in a secondary cycle with 

rabbits in the Central Valley during the late summer (Reeves 1990). The mechanisms by 

which the viruses overwinter and are able to persist despite periods of apparent extinction 

are still unclear though they have been the subject of intense study for over 50 years 

(Kramer 1999). There are currently two main hypotheses, one, that WEE overwinters by 

chronic infection of one or more species of birds, and two, that the virus persists between 

seasons in adult mosquitoes. Humans and horses are infected tangentially by mosquitoes 

but are dead-end hosts for the virus. Data collected from county health clinics by the 

Encephalitis Virus Surveillance indicating a low rate of infection in humans even during 

periods of elevated enzootic transmission may reflect a lowered rate of mosquito-human 

contact. This reduction in the exposure of humans to mosquito bites is likely due to cultural 

factors like the prevalence of televisions and air conditioners that encourage the population 

to spend more time indoors during dusk, the main period of mosquito activity. Expanded 

mosquito control and water management programs have also reduced Culex tarsalis populations. 

Mosquitoes

The mosquito species identified by the District for monitoring and control at the Refuge are 

Culex tarsalis, Anopheles freeborni, Aedes vexans, Aedes melanimon, Aedes nigromaculis,

and Aedes increpitus. Culex 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). 

Anopheles freeborni can transmit the malaria parasite to humans and is common in the 

rice growing regions of California. Aedes melanimon is involved in the encephalitis virus 

(sleeping sickness) cycle, and is considered a secondary vector for WNV (SYMVCD 2004). 

Mosquito Biology

Mosquitoes are dipterans with aquatic immature stages and an aerial adult stage. Eggs 

must come in contact with water in order to hatch. Mosquitoes have four aquatic larval 

stages (instars) plus an aquatic pupal stage. The aerial adult emerges from the pupal stage 

onto the surface of the water, expands its wings, hardens its exoskeleton, and flies off. It 

takes from three to 12 days for a mosquito to complete its life cycle in northern California, 

depending on seasonal and environmental factors and the particular mosquito species 

involved. In general, the warmer the ambient temperature, the fewer days are required 

from hatching to emergence. 

Ochlerotatus (floodwater) mosquitoes (O. melanimon, O. nigromaculis, O. vexans) 

The Aedes life cycle is initiated with the flooding of ground that has undergone a dry 
410 Stone Lakes NWR Comprehensive Conservation Plan

period. In the Sacramento Valley, the dry period may occur at any time from May through 

September. Once flooded, eggs that had been laid during the previous wet cycle hatch, 

pupate, and emerge as adults. Gravid females lay their eggs singly on damp soil, in leaf 

litter, in cracks in the soil, at the edges of drying ponds, or at the bases of grasses and 

other plants. Each female lays approximately 150 eggs per ovarian cycle. These eggs are 

very drought resistant, which allows them to survive during the summer. These mosquito 

species overwinter in the egg stage and to a much lesser extent in the larval stage. Aedes

mosquitoes (primarily A. melanimon) are the most abundant produced on Refuge habitats, 

primarily during late summer and fall flooding. Numerous A. melanimon can also be 

produced as a result of wetland irrigations in late spring through early summer. During 

these times, mosquito eggs hatch, pupate, and reach the adult stage rapidly. Ochlerotatus

are most numerous on Refuges during the fall when the majority of wetlands are flooded. 

Multiple hatchings of eggs commonly occur due to the timing of the different broods of eggs 

and differences in flooding schedules for individual areas. During the warmer months, it 

generally takes 3-10 days for these mosquitoes to develop from egg to adult (i.e., after initial 

flooding). Adult females of the three species of Aedes mentioned above are all aggressive, 

relative to other species, and are biters of primarily mammals. During the day, females will 

bite if disturbed or if a host presents itself, but generally are more active at dusk. Biting and 

swarming (mating) activities are typically crepuscular (occurring at twilight). When newly 

emerged, these mosquitoes do not readily move away from their emergence sites. As they 

age, however, they will move about much more freely. Although all three species of Aedes

are produced in this area, A. melanimon has consistently been the most numerous and the 

cause of most concern as both as a nuisance and a public health risk. Aedes mosquitoes have 

been documented as secondary vectors for California Encephalitis and WNV. 

Culex tarsalis (Encepalitis Mosquito)

Culex tarsalis occur in northern California in very large numbers during the summer. 

Females lay their eggs on the water surface in bunches called rafts. Each raft contains 

around 100-150 eggs, hatching about 24 hours after being laid. The immature stages can 

be found in almost any source of water except treeholes. During the summer, development 

from egg to adult takes about 9 days in the Sacramento Valley. This species is dramatically 

multivoltine (producing several broods), with adults emerging continuously throughout 

the summer. Abundant larva are commonly found in rice fields, poorly drained pastures, 

wetlands, sewer treatment plants, log decks, dairy farms, and seepages. Within Refuge 

habitats, C. tarsalis can be abundant in seasonal marsh and watergrass production units 

that have been flooded for more than two weeks during the fall. Adults spend daylight hours 

resting in secluded places such as cellars or animal burrows. Biting and swarming activities 

are crepuscular. Peak populations occur in late June or early July. C. tarsalis are primarily 

biters of birds, but will bite humans, livestock, and other mammals if the opportunity 

presents itself. C. tarsalis are strong fliers. Mark-release-recapture studies conducted in 

Sutter County in 1989 and 1990 showed that adult C. tarsalis could move up to 3 miles in just 

one night. C. tarsalis are the primary vector for Western Equine Encephalitis, St. Louis 

encephalitis, and WNV in humans.

Anopheles freeborni 

A. freeborni also occur in northern California and are numerous during the summer. Rice 

fields are the primary production areas for this species although the immature stages are 

also found in ditches, seepages, sloughs, and wetlands. Females lay their eggs singly on the 

surface of the water where they hatch approximately 24 hours later. On the average, it takes 

12 days for A. freeborni to develop from egg to adult in the Sacramento Valley. A. freeborni

are most abundant in persistent wetlands, thus Refuge perennial marsh can produce A. 

freeborni during the summer months. However, relatively stable water levels and a relative 

abundance of mosquito predators (fish, dragonflies, and aquatic beetles) tend to minimize 
Stone Lakes NWR Comprehensive Conservation Plan 411

adult mosquito emergence from these habitats.

This species is also multivoltine, with the ability to produce a continuous supply of newly 

emerged adults under the right habitat conditions. Adults rest during the day and engage 

in biting and swarming activities during crepuscular periods. In the fall, females go into 

diapause (overwintering stage) until January, February, or March when they come out of 

diapause and seek blood meals on warm days. After obtaining a blood meal, many females 

resume their overwintering stage until April or May. A. freeborni populations peak in late 

July or August. The females will readily bite humans and livestock. Area-wide, they are 

the most common nuisance mosquito for humans. Studies on A. freeborni in California have 

indicated long flight ranges from source areas. Work done in Sutter County found that this 

species could fly 2-3 miles in one night. This species is considered to be the most important 

vector of malaria in the Western United States.

III. Monitoring Mosquito Populations 

District monitoring activities are designed to assess the abundance of immature (larvae and 

pupae) and adult mosquito populations. Monitoring activities conducted on the Refuge may 

include: larval sampling, adult light and host-seeking traps and adult leg counts. Monitoring 

by District staff may occur as often as 3-4 times per week during the summer irrigation 

(May 1st-July 31st) and fall flood up (August 1st-October15th). If temperatures are above 

average beyond October 15, District staff may continue to require access to the Refuge for 

monitoring. 

Light and carbon dioxide traps are used to capture adult mosquitoes for monitoring 

purposes. Dip counts are used to estimate the numbers of immature mosquitoes and to 

determine the need for larval mosquito control. The dipper method entails using a longhandled ladle (ca 500 ml) called a dipper to collect water samples from possible mosquito 

sources. Captured immature mosquitoes are identified taxonomically as precisely as 

possible. All Refuge units supporting wetlands or irrigated land potentially may be 

monitored using the dipper method. However, units supporting managed wetlands would 

be targeted. Sampling locations for larvae may include wetland margins and shorelines and 

riparian habitats for adults.

As provided for in the MOU, the monitoring activities described above are conducted under 

a Special Use Permit (SUP) that the Refuge intends to continue issuing annually to the 

District. 

1. Larval Mosquito Thresholds 

Guidelines for control of immature or larval mosquitoes follow integrated pest management 

principles and are defined in a District Mosquito and Mosquito-Borne Disease Management 

Plan (Appendix I), available on their website (http://www.fightthebite.net) (Boyce 2005). In 

keeping with the MOU, the District requests annual approval from the Refuge to control 

mosquitoes by treating areas where larval stages of Culex tarsalis, Aedes melanimon, A. 

nigromaculis, Anopheles freeborni or other Aedes spp. may exceed thresholds. According 

to the District Management Plan, the threshold for initiating a larval control response will 

be a density of 0.1 mosquito larvae per 350-ml dipper of water for all species. 

2. Adult Mosquito Thresholds

The District Management Plan defines criteria for five possible levels of adult mosquito 

activity and control responses (Appendix II). The thresholds for Level 1 (Standard or 
412 Stone Lakes NWR Comprehensive Conservation Plan

Routine) adult mosquito control are 10 Culex tarsalis female mosquitoes per light trap night 

or 100 per CO2 baited trap per night. For Aedes spp. the thresholds for Level 1 control are 

50 female mosquitoes per light trap night or 150 per CO2 baited trap per night. Under Level 

I, the thresholds for landing (leg) count collections are exceeded when two or more Aedes

or Ocheloratus spp. land on an individual during a one-minute interval. Level 1 control in 

the District Management Plan is consistent with Level 1 (Normal Season) in the California 

Department of Health Services Mosquito-Borne Virus Surveillance and Response Plan (CA 

Dept. of Heath Services 2004).

The District Management Plan calls for a Level 2 control response when a mosquito-borne 

virus is confirmed from a dead bird or mosquito pool within District boundaries. The 

threshold for levels 2-5 adult control is 10 Culex tarsalis or Cx. Pipiens female mosquitoes 

per light trap night or 25 per CO2 baited trap per night. For Aedes spp. the thresholds for 

Level 2-5 control responses are 25 female mosquitoes per light trap night or 50 per CO2

baited trap per night. Level 2 control in the District Management Plan is equivalent to 

Level 2 (Epidemic Conditions) in California Department of Health Services Mosquito-Borne 

Virus Surveillance and Response Plan (CA Dept. of Heath Services 2004). According to the 

District Management Plan, levels 2-5 adult treatment thresholds remain at the reduced level 

until control activities are terminated for the mosquito season. The thresholds used by the 

District are based on historical monitoring that indicate all mosquitoes have the potential 

to transmit a wide range of diseases. Thresholds also minimizes annoyance levels to nearby 

communities from adult mosquitoes.

IV. Surveillance of Mosquito-Borne Disease 

Vectorborne disease surveillance and associated health threat determinations are made by 

the California Vectorborne Disease Surveillance System (CVDS), a cooperative project of 

the Mosquito and Vector Control Association of California, the California Department of 

Health Services (CDHS), and the University of California at Davis. The UC Davis Center 

for Vectorborne Diseases (CVEC) analyzes samples collected from mosquito pools, sentinel 

chickens and dead birds and publishes results in the California Arbovirus Surveillance 

Bulletins. The samples are collected by the District.

The District arbovirus surveillance program includes testing of mosquito populations, 

sentinel chickens and wild birds for WEE, SLE and WNV. The information generated 

by the encephalitis program provides an early indication of local arboviral activity. Small 

populations of mosquitoes from sites that have a history of disease activity are sampled 

and tested by the mosquito abatement district. Carbon dioxide traps attract and capture 

mosquitoes which are subsequently identified, sorted and grouped into pools. The pools are 

sent to the CVEC where they are tested for encephalitis viruses. Mosquitoes are collected 

annually from March to November.

As part of monitoring conducted by the District for the presence of mosquito borne public 

health diseases, a sentinel chicken flock is maintained on private property adjacent to the 

Refuge Headquarters Unit. Service Region 1 policies prevent placement of sentinel chicken 

flocks on wildlife refuges because of the risk of avian diseases passing from chickens to 

migratory birds. Sentinel chickens are exposed to the environment and to mosquitoes 

moving through the area that may choose to feed on them. Regular blood samples are 

periodically taken from the chickens to detect any mosquito-vector pathogen activity. Once 

the flock exhibits positive viral titers and sero-conversion occurs, the California Department 

of Health Services is alerted to the potential threat to public health due to mosquito borne 

diseases.
Stone Lakes NWR Comprehensive Conservation Plan 413

For approximately the last ten years, Refuge staff and the District have conducted a 

collaborative research effort to collect blood samples from resident and migratory birds 

captured on the Refuge. The wild bird sera samples are processed and tested for the 

presence of WEE, SLE and WNV virus antibodies at the District laboratory. These 

cooperative efforts also provide the Service with important data regarding the status of 

migratory bird populations occurring on the Refuge.

Contacts:

Dave Brown Manager, Sacramento-Yolo Mosquito and Vector Control District

8631 Bond Road 

Elk Grove, CA. 95624 

Phone (916) 685-1022 

Fax (916) 685-5464 

Chris Voight Executive Director, The Mosquito and Vector Control Association of California 

cvoight@mvcac.org 

Dr. Vicki Kramer, Chief, Vectorborne Disease Section, California Department of Health 

Services 

vkramer@dhs.ca.gov 

Dr. Bruce F. Eldridge, Emeritus Professor, University of California at Davis

bfeldridge@ucdavis.edu 

For information on sentinel chicken flock data: 

Mr. Stan Husted, Senior Public Health Biologist, Vectorborne Disease Section, California 

Department of Health Services

shusted@dhs.ca.gov 

For information on mosquito virus isolations: 

Barbara Cahoon-Young, Laboratory Manager, Arborvirus Research Laboratory, UC Davis 

Center for Vectorborne Disease Research

bcahoon@ucdavis.edu 

Reporting

1. The District will notify the Refuge Manager in the event of detection of virus activity 

within or near the Refuge and the method of disease surveillance yielding positive results. 

2. Refuge staff will participate in collections of wild bird sera for testing and will monitor any 

unusual bird die-offs that may be caused by WNV or other diseases. Wild bird mortality 

due to WNV can provide an early warning of the risk of transmission to the public via 

mosquitoes.

V. Treatment Options 

Mosquito control at the Refuge follows an ordered succession, using nonchemical treatments 
414 Stone Lakes NWR Comprehensive Conservation Plan

first (i.e., wetland and water delivery system design, water control strategies, vegetation 

management, mosquitofish, guppies, and other biological agents, etc.), resorting to chemical 

treatment only when necessary, as determined through standard mosquito monitoring 

procedures. Among chemical treatments, adulticides will be used as a last resort. Refuge 

staff work with the District to minimize production of mosquitoes on the Refuge by means of 

habitat management and biological controls and are mindful of abiotic sources of mosquito 

production (e.g., tanks, buckets, equipment holding water) and promptly eliminate them if 

discovered.

Habitat Management

Refuge habitat management techniques that support mosquito abatement consist of: (1) 

design of managed wetlands, (2) efficient water management, and (3) physical manipulation 

of vegetation. These are mostly preventative measures to eliminate or reduce mosquito 

breeding habitat or conditions before it develops. If habitats were managed entirely for 

mosquito abatement, wildlife habitat values would be compromised. Therefore, Refuge staff 

strive to incorporate management techniques for mosquito abatement into ongoing wildlife 

habitat efforts. In an officially determined health emergency, mosquito abatement would 

become a higher priority than habitat management.

Wetland Design and Water Management

Water management techniques for minimizing mosquito production include timing and 

duration of flooding, the speed at which individual units are flooded up, irrigated, or drawn 

down and the stability of water levels. The Refuge is only able to conduct efficient water 

management on managed wetlands impoundments with pumps and water control structures 

where they can be manipulated to reduce mosquito production. These occur on the Beach 

Lake, Headquarters, and South Stone Lake units. Elements incorporated into the design 

of these wetlands that promote minimizing mosquito breeding include contouring of 

wetland margins, construction of drainage swales, and sizing of water control structures 

for relatively rapid flood up and de-watering. Steeper sloped wetlands support narrower 

perimeter margins where warm, shallow, vegetated conditions provide optimal breeding 

habitat for many species of mosquitoes.

Managed permanent and summer water wetlands produce the fewest numbers of 

mosquitoes and pose the least concern for the District. Permanent wetlands are flooded to a 

depth of approximately three feet which minimizes their use by floodwater mosquitoes and 

encourages abundant populations of mosquito predators (e.g., fish, dragonflies). Deep, open 

water provides water circulation and generates wave action that reduces micro-habitats 

suitable for mosquito breeding. 

Seasonal wetland impoundments with water control structures are managed to provide 

wildlife habitat while minimizing the potential for mosquito production. Water delivery 

infrastructure is sized for rapid flood up, irrigations, and draw down, providing at least 

two means by which mosquito production is reduced. Slow irrigations, especially over 

large units, usually result in multiple hatches of adult mosquitoes. For example, if it takes 

five days to inundate a unit, a new hatch of eggs (i.e., typically Aedes melanimon) could 

be produced every day resulting in five separate cohorts of larvae/pupae and subsequent 

adult mosquitoes emerging over a five day period. The alternative is to flood up rapidly, 

covering the entire unit within one day if possible. This will not reduce the overall amount 

of mosquitoes produced but it will result in a more synchronous egg hatch and adult 

emergence. This will facilitate a more efficient control effort, requiring fewer applications 

for the same objective. 

The timing of the fall flood up can substantially affect both mosquito production and wildlife 

habitat values. Delaying the initial fall flood up also delays associated initial mosquito 

production and may reduce the need for mosquito abatement if temperatures have already 

dropped sufficiently to discourage mosquitoes. Historically, Sacramento Valley wetlands 
Stone Lakes NWR Comprehensive Conservation Plan 415

flooded naturally and much later, in the fall or early winter, based largely on the Sacramento 

River overflowing its banks. However, current managed wetland flooding regimes are 

dictated largely by water availability through irrigation districts and the need to provide 

wetlands for early migrating waterbirds during August-September. For example, providing 

roosting habitat for sandhill cranes is a priority at the Refuge which requires flooding 

up by mid-September, when they first arrive in the valley. Though this practice conflicts 

with District abatement recommendations, sandhill crane habitat considerations are given 

precedence over mosquito control. In the event of a threat to public health and/or unusually 

warm fall temperatures that would encourage mosquito production, delaying fall flood up 

remains an option.

Effective communication between Refuge staff and the District remains a critical 

requirement for coordinated mosquito management. In addition to submitting an annual 

summary of planned water management to the District, Refuge staff provide advance 

notifications of flood ups and irrigations so mosquito monitoring and possible treatments can 

be scheduled at an optimal time. Such notifications can result in applications of adulticides 

not being required since the District then has an opportunity to control larval populations, 

thus controlling adult emergence rates. For example, the Refuge attempts to flood wetlands 

early in the week so that mosquito hatches do not occur over the weekend when District staff 

are not in the field.

Physical Manipulation of Vegetation

Vegetative structure in wetlands provides habitat features that generally favor mosquito 

production. The benefits of vegetation include egg-laying sites, protection from the 

elements, and escape cover. The literature suggests that reduction of vegetation by burning 

or mowing (Batzer and Resh 1992) can reduce mosquito production significantly. 

Mowing, herbicide applications, disking, or burning are the most common methods of 

reducing accumulations of vegetation in wetlands on the Refuge. Depending on the extent 

of vegetation they support, managed wetlands may be manipulated during the dry season to 

support a target mix of open water to emergent vegetation: approximately 50% vegetation 

to 50% open water. These manipulations improve wildlife habitat by promoting wetland 

plants of more food value for migratory waterfowl, increasing edge habitat, and the overall 

openness of wetland units, making them more attractive to shorebirds and species such 

northern pintail, green-winged teal, and sandhill crane. These treatments also reduce 

the extent of mosquito breeding habitat and improve accessibility to mosquito larvae by 

mosquito fish and other natural predators. Seasonal wetlands lacking in water control 

structures cannot be as easily managed but wetland perimeters may be mowed or disced 

both to improve conditions for mosquito fish and as well as to increase their value for 

waterbirds.

Major portions of Refuge waterways (e.g., South Stone Lake, SP Cut) have been invaded 

by the invasive aquatic plants, water hyacinth and Brazilian elodea (Egeria densa). Left 

unchecked, these continuous floating or submerged mats of vegetation can encourage 

mosquito production by providing harborage from predation, concentration of organic 

foods, and interference with wave action and water circulation. The Refuge was a founding 

member and has the lead role in the Stone Lakes Basin Water Hyacinth Control Program, 

along with the District and the Sacramento Regional County Sanitation District. This 

program contributes to both mosquito abatement and wildlife habitat improvement goals.

In summary, habitat management techniques promoting mosquito abatement include:

• Construct wetland impoundments with appropriate slopes and adequate water 

management capacities

• Flood up/irrigate quickly to discourage multiple hatches
416 Stone Lakes NWR Comprehensive Conservation Plan

• Maintain a depth of 2-3 feet of water in permanent wetlands

• Control emergent vegetation to maintain 50 percent open water in managed wetlands

• Disc/mow pond perimeters in seasonal wetlands to maintain open water and access by fish

• Control invasive aquatic weeds 

• Notify the District of planned flood up/irrigation events

Biological Controls

Reducing production of mosquitoes in a wetland ecosystem is partially dependant upon 

maintaining a diversity of habitats that support various predators and parasitic species that 

can then control mosquito populations. Predators and parasites can take sizable numbers 

of mosquitoes but if conditions support the rapid development of mosquitoes, then natural 

predation can be augmented by the addition of insectivorous (insect eating) fishes. The 

District has introduced three species of insectivorous fish to the Refuge, mosquito fish 

(Gambusia affinis), guppies (Poecilia reticulata) and the native threespine stickleback 

(Gasterosteus aculeatus).

Mosquitofish

Mosquitofish have played an active role in mosquito larvae control at refuges within 

California’s Sacramento Valley over the last twenty years. Mosquitofish exhibit a 

tremendous tolerance for a wide range of water temperatures. Previously acclimated 

fish may tolerate minimum and maximum temperatures of 33° and 104°F (0.6° and 40°C), 

although sudden drastic changes of temperature are often lethal. Preferred temperatures 

appear to lie between 77° and 86°F (25° and 30°C). When surface water temperatures 

approach higher lethal limits, mosquitofish usually swim down to cooler water strata. 

Conversely, in the cooler seasons mosquitofish will move into shoal areas to reach the sunwarmed shallow waters. Other environmental factors that influence mosquito fish survival 

include densities of mosquito larvae, aquatic vegetation, availability of alternative forage 

organisms, presence of predaceous bird and fish populations, water depth and flow patterns, 

and several water quality criteria. For the fish to be effective, there must be no limitations 

to their normal distribution, rapid reproduction, and population recruitment. In general, 

mosquitofish are stocked in very small numbers because they quickly reproduce to the 

maximum population levels that a particular habitat may sustain.

Mosquitofish are transported by tanker truck directly to mosquito sources. Primary 

stockings of fish in semi-permanent wetlands are usually conducted at a minimal initial rate 

of 0.1 lb per acre. When necessary, these applications are augmented up to 1.0 lb per acre, 

based on larval dipping data. The District has stocked Refuge waters with mosquitofish 

every year since 1996. Most of the mosquitofish have been planted in the Beach Lake Unit, 

but some have also been placed in small ponds on the Sun River and Beach Lake properties.

Guppies and Threespine Sticklebacks

The District is evaluating the use of guppies and threespine sticklebacks for mosquito larvae 

control. Literature suggests that guppies will do an excellent job of controlling mosquitoes 

during the summer months but will not survive the cold winter months. Using this species in 

areas that are prone to winter flooding will ensure that these fish will not impact threatened 

or endangered species occurring within the floodplain. Threespine sticklebacks prefer to 

feed on benthic organisms rather than on the surface where mosquito larvae are found, 

but where the benthic community is insufficient, the Sticklebacks will expand their feeding 

range to the surface. Sticklebacks were only planted at the Refuge in 2001, while guppies 

were used in 2002 and 2003.

Chemical Controls

Larvicides/Pupacides

The District proposes to control mosquitoes by treating areas infested with larval stages 

of Culex tarsalis; Aedes melanimon, A. nigromaculis, Anopheles freeborni and Aedes spp. 
Stone Lakes NWR Comprehensive Conservation Plan 417

The District would use the biological larvicides Bacillus thuringiensis isrealensis (Bti) 

and Bacillus sphaericus (Bsp) and the insect growth inhibitor methoprene. Use of the 

petroleum distillate Golden Bear (GB1111) as a pupacide was discontinued after 2000 and 

has been replaced with the monomolecular film Agnique. These treatments would be applied 

via ground methods. Based on December 2005 Service Delegation of Approval Authority 

for the California Nevada Operations (CNO) area, refuge managers now have authority to 

approve use of Bti, Bsp, methoprene, and Agnique.

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 

therefore be ingested by the target insect to be effective. It is most effective on younger 

mosquito larval instars but does not affect pupae or adult mosquitoes. The District prefers 

to use Bti because of the low impacts to the environment and non-target organisms and its 

effectiveness in reducing the numbers of mosquito larvae. The Bti formulations Vectobac 

12AS or Vectobac G would be employed at the Refuge by the District. Bti may be applied at 

the Refuge between March and October.

Like Bti, Bsp is a microbial insect pathogen with a similar mode of action (Walton 1998). 

Formulated Bsp products used as mosquito larvicides consist of bacterial spores and protein 

endotoxins. The granular formulation of Bsp, Vectolex CG, would be applied by the District. 

Both Bti and Bsp may be applied as a spot treatment to small areas or broadcast over larger 

areas. Use of Bsp is permitted between June 1 and September 30 and applications would 

likely be made within 7-10 days of initial flooding to control third and fourth instar larva.

Methoprene is a synthetic insect growth regulator (IGR) 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 but 

does not affect pupae or adult mosquitoes (ETN 1996a). Treated larvae will pupate, but will 

not emerge as adults. The District proposes to use the formulated methoprene product 

Altosid in pellets or A.L.L. Growth Regulator. Use of methoprene is permitted between 

June 1 and September 30.

The monomolecular film, Agnique, reduces water surface tension. This interferes with 

larval orientation at the air-water interface and/or increases wetting tracheal surfaces, thus 

suffocating the organism. As the film spreads over the water surface, it tends to concentrate 

mosquito pupae, which may increase mortality from crowding stress (Dale and Hulsman 

1990). Use of Agnique is permitted between June 1 and September 30.

Area Subject to Larvicides

Applications of larvicides may occur in managed permanent wetlands (106 acres), irrigated 

pastures (490 acres) and occasionally perennial wetlands (193 acres), totaling approximately 

790 acres. The shorelines of open water areas may be treated. In addition, the District will 

treat ditches, culverts and low areas not classified as wetlands. 

As a result of IPM practices and cooperation between the Refuge and the District, larval 

control applications on the Refuge have been limited to small acreages during any single 

treatment (less than five acres). The total Refuge acreage that may be treated varies with 

rainfall conditions each year. During drought years mosquito populations tend to be low, and 

during wet years mosquito populations tend to be high. From 2000-2004, the range in total 
418 Stone Lakes NWR Comprehensive Conservation Plan

acreage treated varied from a low of 104 acres in 2000 to a high of 477 acres in 2004. The 

majority of the treatments occur from August to October, but in some years applications of 

Bti have begun as early as March and have extended into November. 

Adulticides

If efforts to control immature mosquitoes fail to prevent the adult mosquito population 

from exceeding thresholds, and a documented historical or current health threat exists, 

the District proposes to treat infested areas with a mosquito adulticide. The District has 

requested annual approval for use of liquid formulations of synthetic pyrethrins, such as 

Pyrenone 25-5 or Pyrocide 7338. The District also requests and has received approval for 

use of the adulticide Trumpet (Naled) but it has not been used on the Refuge to date. Use 

of all adulticides is limited to June 1 through September 30, with a possible extension if 

unusually hot weather occurs together with a documented public health threat. Based on 

the December 2005 Service Delegation of Approval Authority for the CNO area, refuge 

managers have authority to approve use of pyrethrins for controlling mosquitoes near 

facilities used by staff and visitors and in terrestrial sites (not aquatic sites or wetlands). 

Approval of use of pyrethrins in aquatic or wetland settings or Trumpet necessitates 

submittal of Pesticide Use Proposals to the CNO and Washington offices. 

Pyrethrins are non-systemic contact poisons which quickly penetrate the nerve system 

of the insect and cause paralysis and subsequent death (ETN 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). Trumpet (Naled) is a non-systemic, broad-spectrum 

organophosphate insecticide which affects the nervous system of adult mosquitoes and 

other insects by cholinesterase inhibition. When treatments occur, Pyrethrins and Trumpet, 

would be applied as an ultra-low volume (ULV) mist by ground. To minimize pesticide drift, 

dispersing vehicles follow routes on existing roads set up to fog downwind or outside buffers 

of 300 feet from areas supporting listed or proposed special status species. All chemical 

applications occur when wind speeds are between 2 and 8 mph. 

Between 1994 when then Refuge was established and 2004, adult mosquito applications only 

occurred once in 1998 to five acres (0.09 gallons of Scourge) and once in 1999 to four acres 

(0.05 gallons of Pyrocide 7338). Both treatments were ULV ground applications at the same 

location, a drainage channel on the Headquarters Unit. That adulticides were utilized so 

infrequently, attests to the level of cooperation between District and Refuge who initiated 

water management and larval control measures to discourage mosquito production and adult 

emergence. 

In 2005, West Nile Virus (WNV) became established in Sacramento and Yolo counties, 

triggering more aggressive and widespread mosquito control efforts. In August of 2005 

the number of human WNV cases and rate of infected adult mosquitoes were so high that 

SYMVCD initiated aerial applications of pyrethrin over significant portions of Sacramento 

County. The Refuge received ultra-low volume (ULV) ground applications of pyrethrin on 16 

occasions between July 28 and October 12, 2005. As of August 18, 2006, 16 human cases of 

WNV have been documented in Sacramento and Yolo counties (Table 1) and the Refuge has 

had adulticides applied 12 times beginning on June 27.
Mosquito Fish

Methoprene

Golden Bear

Pyrethrin Adulticides

Bti, Bsp

Land Status &

Acquisition Year

Owned in Fee Title

Easement/Agreement

Non-Refuge Lands

Note: Points may represent

multiple treatment events.

0 0.25 0.5

Miles

0 0.5 1

Kilometers

Stone Lakes

Figure 1. Distribution of Mosquito

Abatement Treatments 1996-2000

Map Date 1/07

National Wildlife Refuge

2003

2004

1998

2004

1994

1994

1997

1996

2000

1995

1999
Mosquito Fish

Methoprene

Pyrethrin Adulticides

Bti, Bsp

Land Status &

Acquisition Year

Owned in Fee Title

Easement/Agreement

Non-Refuge Lands

Note: Points may represent

multiple treatment events.

0 0.25 0.5

Miles

0 0.5 1

Kilometers

Stone Lakes

Figure 2. Distribution of Mosquito

Abatement Treatments 2001 - 2004

Map Date 1/07

National Wildlife Refuge

2003

2004

1998

2004

1994

1994

1997

1996

2000

1995

1999
Mosquito Fish

Methoprene

Pyrethrin Adulticides

Bti, Bsp

Land Status &

Acquisition Year

Owned in Fee Title

Easement/Agreement

Non-Refuge Lands

Note: Points may represent

multiple treatment events.

0 0.25 0.5

Miles

0 0.5 1

Kilometers

Stone Lakes

Figure 3. Distribution of 2005

Mosquito Abatement Treatments

Map Date 1/07

National Wildlife Refuge

2003

2004

1998

2004

1994

1994

1997

1996

2000

1995

1999
Mosquito Fish

Methoprene

Pyrethrin Adulticides

Bti, Bsp

Land Status &

Acquisition Year

Owned in Fee Title

Easement/Agreement

Non-Refuge Lands

Note: Points may represent

multiple treatment events.

0 0.25 0.5

Miles

0 0.5 1

Kilometers

Stone Lakes

Figure 4. Distribution of 2006

Mosquito Abatement Treatments

Map Date 1/07

National Wildlife Refuge

2003

2004

1998

2004

1994

1994

1997

1996

2000

1995

1999
Stone Lakes NWR Comprehensive Conservation Plan 423

VI. 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. The possible effects of the larvicides Bacillus spp. and 

methoprene, the pupacide Agnique, and the adulticides will be discussed separately.

Larvicides

Bacillus thuringiensis isrealensis (Bti) 

Bti has practically no acute or chronic toxicity to mammals, birds, fish, or vascular plants 

(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. 

Bacillus sphaericus (Bsp)

Bsp has slight to practically no acute mammalian toxicity, practically no acute avian toxicity, 

slight to practically no acute fish toxicity, and slight aquatic invertebrate toxicity (USFWS 

1984, and FCCMC 1998). Insecticidal activity may persist longer than 20 days because 

Bsp can reproduce and sporulate in larval cadavers (Becker et al, 1995) and can retain 

its larvicidal properties after passing through the gut of a mosquito. Bsp is insoluble in 

water. Spores and toxin become suspended in the water column and retain insecticidal 
424 Stone Lakes NWR Comprehensive Conservation Plan

activity in water with high organic matter content and suspended solids. Because Bsp is a 

more recently developed larvicide than Bti, there are fewer studies that have examined the 

non-target effects of this pesticide. The data available, however, indicate a high degree of 

specificity of Bsp for mosquitoes, with no demonstrated toxicity to chironomid larvae at any 

mosquito control application rate (Mulla, 1984, Ali, 1986, Lacey, 1990, and Rodcharoen, 1991). 

Therefore risks to sensitive wildlife resources resulting from direct exposure to a single 

Bsp application and indirect food chain effects are expected to be negligible. However, the 

ability for a population to re-colonize a wetland following multiple larvicide treatments would 

depend on the intensity and frequency of applications at different spatial scales.

Agnique (Monomolecular film)

Monomolecular film has practically no acute mammalian or avian toxicity, and slight acute 

fish toxicity (USEPA 2000, USFWS 1984). The risk quotient for mammals is well below 

the EPA endangered species level of concern (LOC) indicating negligible risk resulting 

from direct exposure, Table 2 (Urban and Cook 1986). Risk quotients for birds and fish 

exceed EPA endangered species LOCs indicating a hazard to those taxa resulting from 

direct exposure. Risk to fish is limited by the insolubility of monomolecular film in water. 

Monomolecular film is insoluble in water, average persistence in the environment is 5 to 14 

days. Indirect effects to animals dependent on invertebrate food resources are possible 

resulting from a reduction of those resources caused by monomolecular film. The magnitude 

of the impact would depend on the aerial extent of the treatment, the number of treatments, 

treatment frequency, and the location of the treatment relative to the areas used by 

invertebrate feeding animals. 

Table 2. Monomolecular film risk quotients.

Animal Acute toxicity (ppm) EEC (ppm) RQ LOC (ES)

bird > 5000 (8 D LC 50) 850 (short grass) 0.2 0.1

fish 98 (96 hr LC 50) 2600 (6" water) 26.5 0.05

mammal >20,000 (LD 50) 850 (short grass) 0.004 0.1

EEC calculated using a rate of 0.5 gal/ac (3.6 lbs ai/ac)

LD 50 for mammals converted to 1 Day LC50 using a conversion factor of 0.1 for RQ calculation 

Methoprene

Methoprene has moderate acute fish toxicity, slight acute avian toxicity, and practically no 

acute mammalian toxicity (USEPA 2000, and USFWS 1984). In mallard ducks, dietary 

concentrations of 30 parts per million (ppm) caused some reproductive impairment (USEPA 

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 (USEPA 1991). Up to 95 percent of the residue in fish 

was excreted within 14 days (USEPA 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 (Table 3) 

(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 

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 
Stone Lakes NWR Comprehensive Conservation Plan 425

highly toxic to aquatic invertebrates with a 48 hour EC50 (the concentration of a compound 

where 50 percent of its effect is observed) of 0.89 ppm for Daphnia magna (USEPA 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 (USEPA 1991). Degradation rates are roughly equal in freshwater 

and saltwater systems and are positively correlated to temperature (USEPA 1991). 

Adulticides

There are only two general classes of mosquito 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. 

One organophosphate, Trumpet (Naled), is approved for use at the Refuge in the past but 

not applied to date. The two pyrethroid products approved for use at the Refuge, Pyrenone 

25-5 and Pyrocide 7336 are both synthetic pyrethrins.

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). Pyrethrins are toxic to all invertebrates, but the method of application via ultra-low 

volume atomizer limits toxicity and contact with non-targets. To minimize pesticide drift, 

applications would take place during the evening hours, when wind speeds are reduced and 

temperatures decreased; this is also the period when mosquito activity is the greatest.

Naled is a fast acting, nonsystemic contact and stomach organophosphate insecticide used 

to control aphids, mites, flies, and mosquitoes. Naled is highly to moderately toxic via the 

oral route. It is moderately toxic through skin exposure, may cause skin rashes and skin 

sensitization and may be corrosive to the skin and eyes. Naled is highly to moderately toxic 

to birds. The reported acute oral LD50 (lethal dose 50, the dose of a substance which is fatal 

to 50% of the test animals) for naled is 52 mg/kg in mallard ducks, 65 mg/kg in sharp-tailed 

grouse, 36-50 mg/kg in Canadian geese, 120 mg/kg in ring-neck pheasants. Naled is highly 

to moderately toxic to fish and may be very highly toxic to aquatic invertebrate species 

(ETN 1996). However, Trumpet (Naled) is practically nonpersistent in the environment, 

with reported field half-lives of less than 1 day. It is not strongly bound to soils and is rapidly 

broken down if wet. Soil microorganisms break down most of the naled in the soil. It 

therefore should not present a hazard to groundwater (ETN 1996).

Table 3. Risk assessment for Methoprene.

Animal Acute Tox (ppm) EEC (ppm) RQ LOC (ES)

Bird > 4640 (8 D LC 50) 3.0 (short grass) 0.0006 0.1

Fish 0.4 (96 hr LC 50) 0.01 (6 inches) 0.025 0.05

Mammal > 34,000 (LD 50) 3.0 (short grass) 0.00001 0.1

EEC calculated using a rate of 0.013 lbs ai/ac (1.0 fluid oz/ac Altosid 20 % methoprene)

LD 50 for mammals converted to 1 Day LC50 using a conversion factor of 0.1 for RQ calculation
426 Stone Lakes NWR Comprehensive Conservation Plan

Threatened and Endangered Species

The Refuge provides potential habitat for the following federally-listed species: giant garter 

snake, valley elderberry longhorn beetle, vernal pool tadpole, and vernal pool fairy shrimp. 

Potential impacts to these species from mosquito control activities were addressed in a 

number of previous Intra-Service Section 7 Consultations conducted with the Sacramento 

Fish and Wildlife Office (SFWO):

March 27, 1995: The SFWO concurred with the determination that use of the bacterium 

Bacillus thuringiensis israelensis (Bti) and Altocid® (methoprene) for mosquito control at 

Stone Lakes NWR is not likely to adversely affect the vernal pool fairy shrimp, vernal pool 

tadpole shrimp, giant garter snake, valley elderberry longhorn beetle, Sacramento splittail, 

and delta smelt (SFWO file: 1-1-95-I-0680). 

January 9, 1997: The SFWO concurred with the determination that the use of the bacterium 

Bacillus sphaericus for mosquito control, is not likely to adversely affect the vernal pool 

fairy shrimp, vernal pool tadpole shrimp, giant garter snake, valley elderberry longhorn 

beetle, delta smelt, or Sacramento splittail at the Stone Lakes NWR (SFWO file: 1-1-96-I0639). 

January 31, 2001: The SFWO concurred that pest management activities at the Refuge are 

not likely to jeopardize the giant garter snake, valley elderberry longhorn beetle, vernal pool 

tadpole shrimp, or vernal pool fairy shrimp. (SFWO file:1-1-00-F-0162).

Giant Garter Snake (Thamnophis gigas)

Mosquito control activities in giant garter snake habitat may affect giant garter snakes by 

harassment or injury from vehicle use. The District will only operate vehicles in existing 

roads; therefore, harassment or injury from vehicle use would occur only if snakes are in 

the roadway. Regarding the effects of the proposed pesticides, a Fish and Wildlife Servicesponsored study indicated that the short-term effects of adulticides approved for mosquito 

control on the Sacramento NWRC did not significantly reduce abundance or biomass of the 

snake’s prey items, macro-invertebrates and fish, in treated wetlands (Lawler et al. 1997). 

However, no information is available on the toxicity of the proposed pesticides directly to the 

giant garter snake. Without further information, it must be assumed that exposure of giant 

garter snakes to these chemicals could result in direct impacts, such as loss or sublethal 

effects to individual animals. Adverse effects to the giant garter snake from mosquito 

control activities will therefore be minimized by avoiding any wetland habitat suitable for 

giant garter while applying chemical treatments for control of mosquitoes. The application 

of adulticides by dispersal vehicles will be planned to fog downwind of and outside a buffer of 

300 feet away from permanent emergent wetlands. 

Valley Elderberry Longhorn Beetle (Desmocerus californicus dimorphus)

Adverse effects on the valley elderberry longhorn beetle are not likely since the main 

mosquito abatement period (June-September) does not coincide with the period of adult 

beetle emergence (late April through mid-May or early June). Also, the riparian corridors 

that house the valley elderberry longhorn beetle, generally do not require treatment with 

chemical control agents. If control measures are needed in these areas, some granular 

applications of Bti or Altocid (Methoprene) may be used during February or March when 

adult beetles are not present.

Vernal Pools

The growth regulator Methoprene (Altosid or A.L.L) can have deleterious effects on vernal 

pool shrimp by delaying the development of adult shrimp and thus the number of eggs laid 

before the pools dry up. Because of the effects of Methoprene on fairy shrimp and a lack of 

information on how long the agent remains in the soil, use of the larvicide methoprene within 
Stone Lakes NWR Comprehensive Conservation Plan 427

vernal pools or swales at any time, in either wet or dry conditions, is prohibited (USFWS 

2001). 

The majority of vernal pools and seasonal swales will be dry during the main pesticide 

application period (June-October). In general, naturally functioning vernal pool habitats are 

not significant mosquito-producing habitat and should not require chemical treatments for 

control of mosquito larvae. A study of vernal pools in Sacramento County suggested that 

when mosquito larvae were present in the pools, productivity was limited to a narrow time 

period just prior to drying in late spring. Therefore, vernal pools do not contribute at all 

to mosquito productivity in winter and early spring. In the event that the use of a larvicide 

does become necessary in the vicinity of vernal pools, Bti, which is relatively specific to 

mosquitoes and flies, will be the agent of choice. 

The majority of the vernal pools at the Refuge occur on the Wetland Preserve property 

which became part of the Refuge under a conservation easement in 2004. During the 

spring of 2004, before the conservation easement went into effect, numerous vernal pools 

were treated with Bti. Relatively warm spring temperatures in 2004 likely contributed to 

elevated larval populations, but other factors may also be involved. The mosquito abatement 

district had increased larval monitoring in the area because the Wetland Preserve property 

is adjacent to a new housing development and WNV had recently arrived in Sacramento 

County. Many of the vernal pools in the Wetland Preserve property are man-made 

mitigation pools that may not be functioning as naturally occurring vernal pools would. A 

study of naturally occurring and constructed vernal pools conducted by the District showed 

that while natural vernal pools produced very few mosquitoes throughout most of the wet 

season and then produced a spike in numbers in late April, the constructed vernal pools 

produced significantly more mosquitoes throughout the wet season as well as a spike in 

numbers in April (Wright 1997). In addition, the data suggested that natural vernal pools 

may pose a greater threat of mosquito productivity when associated with constructed pools. 

For these reasons, the mosquito abatement district policy is to dip-sample constructed 

vernal pools and adjacent natural vernal pools. Mosquito abatement treatments near vernal 

pools will be limited to Bti to reduce effects on endangered vernal pool species. Future 

mosquito abatement activities in the Wetland Preserve property will be closely monitored 

by Refuge staff to avoid conflicts between wildlife habitat improvement goals and mosquito 

control goals. 

Wetlands and Waterfowl

The Refuge was established to provide habitat for migratory birds, in particular waterfowl. 

The District will continue to minimize disturbance and non-target effects to wildlife by 

limiting mosquito abatement activities between October 15 and February 15 when the 

majority of migratory bird species arrive on the Refuge. However, since the District 

continues to treat in fall until temperatures have dropped sufficiently to reduce the 

abundance of mosquitoes, in warmer years there may well be a longer period of overlap 

between the arrival of migratory birds and continued mosquito abatement activities. In 

addition, if mosquito thresholds are exceeded, or the presence of WNV or other arboviruses 

are detected in or around the Refuge, then the District may need to extend mosquito 

surveillance and control into late fall.

In some years, most notably 2004, the District has applied Bti or planted mosquito fish as 

early as March when some migratory waterfowl may still be lingering before departing 

on their spring migration. However, Bti has not been found to be toxic to birds (USFWS 

2001). In addition, it has been found that birds are not negatively affected by utilizing 

foods exposed to Bti or methoprene (Niemi et al. 1999). Although physico-chemico data 

and environmental fate data are limiting, Bacillus spp. are virtually non-toxic to mammals, 

birds and fish. Though methoprene has not been shown to pose a threat to birds from direct 
428 Stone Lakes NWR Comprehensive Conservation Plan

exposure, it may affect insectivorous species by decreasing the invertebrate food source. 

However, during the last 8 years methoprene has not been applied prior to June, and was 

applied as late as October in only one instance. Thus, applications of methoprene have not 

directly or indirectly affected migratory birds utilizing the Refuge because migratory birds 

have not been present during mosquito abatement activities.

There is not likely to be much impact on geese and swans from pesticides because they 

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. In contrast, ducks are known to be opportunistic feeders on both plants and 

invertebrates, utilizing 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). Waterfowl in general tend to 

feed on seeds when they reach their wintering areas, perhaps to regain energy lost during 

long flights (Heitmeyer 1988, Miller 1987). Thus any food chain impacts resulting from 

larvicide and adulticide treatments 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.

Birds utilizing the Refuge during the summer months and early fall, when most of the 

mosquito abatement occurs, could have a greater risk of being affected by pesticide 

applications. These species include herons, egrets, white pelicans, mallards and wood ducks. 

The pesticides being applied at the Refuge have not been shown to be toxic to birds, but 

could potentially affect resident waterfowl indirectly by reducing invertebrate food sources. 

Shorebirds could also be of concern, since they feed on a wide variety of invertebrates all 

year, feeding which intensifies at the onset of spring migration. However, 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. 

Jensen et al. (1999) found that no decreases were detected in the biomass or abundance of 

aquatic invertebrates in seasonal wetlands from ultra-low volume applications of pyrethrin, 

permethrin, or malathion. 

VII. Health Threat Determination

For the purpose of allowing the use of certain pesticides or bio-rational pesticides to control 

mosquitoes, a mosquito-borne public health emergency is defined as:

Actual or threatened, imminent outbreak of western equine encephalitis, St. Louis 

encephalitis, West Nile encephalitis, malaria, or other mosquito vector-borne public health 

disease. The presence of WEE, SLE, WNV or malaria viral titers or mosquito pool titers in 

the mosquito population or in sentinel chickens (in accordance with test protocols developed 

by the CDHS Environmental Management Branch, and the U.S. Department of Health and 

Human Services, Center for Disease Control) will confirm that a public health emergency 

exists or is imminent. This threshold will have been met when the mosquito abatement district 

notifies the Refuge manager of a laboratory test that is positive for any of the above viruses. 

The recurring presence of arboviruses in the Central Valley since the 1940s has been well 

documented (Reeves 1987) such that the baseline health threat level at the Refuge is 2-3, 

depending on monitoring. Occurrences of WNV within Sacramento County in humans, 

domestic animals and wildlife are expected to increase in 2005 relative to 2004 (see Disease 
Stone Lakes NWR Comprehensive Conservation Plan 429

History above) based on observed arboviral disease cycles. The health threat level for 

the Refuge is therefore 4-5 (see Table 4) for 2005 and may be elevated to 6-7 if an officially 

determined health emergency is declared due to WNV. Historically, the mosquito abatement 

response has been the same at threat levels 2-3 as in threat levels 4-5, that is, adulticides 

and pupacides have been approved for use by the Service based on the historical health 

threat rather than being reserved for use only when an existing health threat has been 

documented. As a result, mosquito larval control activities since 1994 have been largely 

limited to localized (less than five acres) applications of larvicides and until 2005, only three 

applications of adulticides. 

Table 4. Example of Mosquito-Borne Disease Health Threat and Response Matrix

Current Conditions Refuge Response

Health Threat

Category1

Refuge

Mosquito Populations 2

No documented 

existing or historical 

health threat/

emergency

No action threshold 1 Remove/manage artificial mosquito 

breeding sites such as tires, tanks, or 

similar debris/containers.

Documented 

historical health 

threat/emergency

Below action threshold 2 Response as in threat level 1, plus: 

allow compatible monitoring and 

disease surveillance. Consider 

compatible nonpesticide management 

options to reduce mosquito production.

Above action threshold 3 Response as in threat level 2, plus: 

allow site-specific compatible larviciding 

of infested areas as determined by 

monitoring.

Documented existing 

health threat (specify 

multiple levels, if 

necessary; e.g., disease 

found in wildlife, 

disease found in 

mosquitoes, etc.)

Below action threshold 4 Response as in threat level 2, plus: 

increase monitoring and disease 

surveillance.

Above action threshold 5 Response as in threat levels 3 and 4, 

plus: allow compatible site-specific 

larviciding, pupaciding, or adulticiding 

of infested areas as determined by 

monitoring.

Officially determined 

existing health 

emergency

Below action threshold 6 Maximize monitoring and disease 

surveillance.

Above action threshold 7 Response as in threat level 6, 

plus: allow site-specific larviciding, 

pupaciding, and adulticiding of infested 

areas as determined by monitoring.

1 Health threat/emergency as determined by Federal and/or State/local public health authorities with 

jurisdiction inclusive of Refuge boundaries and/or neighboring public health authorities.

2 Action thresholds represent mosquito population levels that may require intervention measures. 

Thresholds will be developed in collaboration with Federal and/or State/local public health 

authorities and vector control districts. They must be species and life stage specific.
430 Stone Lakes NWR Comprehensive Conservation Plan

VIII. Stipulations and Reporting

1. Every attempt will be made to minimize mosquito production through wetland design, 

habitat (water level and vegetation) management techniques, mosquito fish or other 

non-chemical treatments, before larvicides or adulticides are applied. Among chemical 

treatments, adulticides will be considered a last resort. 

2. In keeping with the MOU, the Refuge will provide the District with an annual summary 

of planned Refuge water management and with notification of timings of flood ups and 

irrigations.

3. As required under the MOU, the District will provide the Refuge Manager with an 

annual operating plan for anticipated mosquito monitoring and control activities that 

may be needed on the Refuge during the upcoming year. The plan will provide for 

Refuge access requirements, control thresholds, and proposed larvicides and adulticides.

4. Mosquito control will be authorized on an annual basis by a Special Use Permit (SUP) 

issued by the Refuge. SUP conditions will reflect any applicable restrictions required 

under approved Pesticide Use Proposals or Section 7 Consultations. 

5. The Refuge will submit to the CNO Office all required Pesticide Use Proposals to 

maximize likelihood of PUP approval prior to onset of upcoming mosquito season.

6. The District will notify the Refuge manager as soon as possible when mosquito larval 

thresholds (see IPM Plan, Figure 5) are exceeded and ground treatments are warranted.

7. When adult thresholds are exceeded, and in the event of a planned adulticiding, the 

District will contact and personally coordinate with the Refuge Manager or Assistant 

Refuge Manager prior to conducting the treatments to ensure control efforts do not 

conflict with routine Refuge operations.

8. The District will continue to consider environmental conditions, including water 

temperature, density of mosquito larvae, and presence of mosquito predators, when 

determining mosquitoes on the Refuge pose a threat to public safety and whether 

treatments are required.

9. To minimize pesticide drift, dispersing vehicles will follow routes on existing roads set up 

to fog downwind or outside buffers of 300 feet from areas supporting listed or proposed 

special status species, including vernal pools.

10. All chemical applications will occur when wind speeds are between 2 and 8 mph.

11. Any applications of mosquito adulticides will occur outside a buffer of 300 from any 

permanent emergent wetlands. 

12. Application of mosquito control measures is to be conducted in accordance with approved 

Pesticide Use Proposals.

13. Mosquito control will be authorized on an annual basis by a Special Use Permit (SUP) 

issued by the Refuge. SUP conditions will reflect any applicable restrictions required 

under approved Pesticide Use Proposals or Section 7 Consultations. 

14. At the end of the season and as required under the MOU, the District will provide the 

Refuge Manager with an annual report summarizing mosquito control activities during 

the previous year.
Stone Lakes NWR Comprehensive Conservation Plan 431

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436 Stone Lakes NWR Comprehensive Conservation Plan

34

Adult mosquito

thresholds exceeded?

Larval mosquito 

thresholds exceeded? 

Yes

No

Yes

Maximize monitoring and disease 

surveillance. PUPs serve as guidance, 

but District implements control as 

necessary to prevent or control 

outbreak for that season. 

No

Site specific adulticiding with 

pyrethroids or resmethrin based on 

ongoing monitoring. Refuge 

manager must confirm prior to 

application of adulticides. 

Stipulations apply.

Continue habitat management 

and biological larval control 

measures. 

Continue biological larval 

control measures to keep adult 

populations low and reduce or 

eliminate need for adulticiding. 

MONITORING

District monitors adult and 

larval mosquito populations 

with larval dips, light traps 

and landing counts from 

March through Oct 

SURVEILLANCE

District monitors disease activity by sampling sentinel chicken flocks, 

mosquito pools, and wild birds. CVEC analyzes samples and CVDS makes 

health threat determinations.

Site specific larval and pupal control 

with insectivorous fish, Bti, Bsp, 

methoprene, or monomolecular film 

as needed based on ongoing 

monitoring. Stipulatins apply. 

Officially Determined 

Health Emergency: 

Threat Level 6-7 

Existing health threat: 

Disease found in wildlife 

or domestic animals: 

Threat Level 4-5 

Historical health threat 

documented in the Central 

Valley: 

Baseline Threat Level 2-3 

SURVEILLANCE

District monitors disease activity by sampling sentinel chicken flocks, 

mosquito pools, and wild birds. CVEC analyzes samples and CVDS makes 

health threat determinations.

Officially Determined 

Health Emergency: 

Threat Level 6-7 

Existing health threat: 

Disease found in wildlife 

or domestic animals: 

Threat Level 4-5 

Historical health threat 

documented 

in theCentral Valley: 

Baseline Threat Level 2-3 

Figure 5. Mosquito Monitoring and Control Protocol
Stone Lakes NWR Comprehensive Conservation Plan 437

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Stone Lakes National Wildlife Refuge

1624 Hood-Franklin Road

Elk Grove, CA 95757

Telephone: 916/775-4421

Fax: 916/775-4407

California Relay Service

TTY: 1 800/735-2929

Voice: 1 800/735-2922

U.S. Fish and Wildlife Service

California/Nevada Operations Office

http://www.fws.gov/cno/

Refuge information: 1 (800) 344-WILD

January 2007