2006-2007

Upper Colorado River Endangered Fish Recovery Program

San Juan River Basin Recovery Implementation Program

Program Highlights
Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 1

Upper Colorado River Endangered 

Fish Recovery Program

and

San Juan River Basin Recovery 

Implementation Program

Balancing Species Recovery with

Water Resource Development and Management

Program Highlights 2006-2007

The Upper Colorado River Endangered Fish Recovery

Program and the San Juan River Basin Recovery

Implementation Program are based on a balanced

approach. Multiple state and federal agencies work cooperatively with public and private interests to recover the endangered Colorado River fishes. Water development and 

management continue in compliance with interstate compacts and all applicable federal and state laws. The recovery

programs provide Endangered Species Act compliance for fulfillment of federal trust responsibilities to American Indian

Tribes and continued operation of federal water and power

projects in accordance with project purposes.

Program Highlights is produced annually to document the recovery programs’ progress toward recovery of the

endangered fishes. This document is not a publication of the U.S. Department of the Interior or its agencies.
2 2006-2007 Program Highlights

Recovering Endangered Fishes in the Upper Colorado and San Juan River Basins . . . . . . . . . . . . . . . . . . . . . . 3

Partners’ Active Commitment and Participation Key to Recovery Programs’ Success . . . . . . . . . . . . . . . . . . . 4

Demonstrated Achievements Draw Bipartisan Support for Endangered

Fish Recovery Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Federal Laws Authorize Cost-Sharing and Show Congressional 

Commitment to Species Recovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Recovery Programs Rely on Recovery Goals to Manage

Actions and Measure Success . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Implementing Innovative Solutions to Manage Water and

Improve River Habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Cooperative Effort to Enlarge Colorado’s Elkhead Reservoir Benefits

People and Endangered Fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Construction Projects to Improve River Habitat Nearly Complete . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 & 11

Reestablishing Fish Populations through Propagation and Stocking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Stocking Efforts Show Encouraging Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Developing Solutions to Manage Nonnative Fishes and Provide

Sportfishing Opportunities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Involving Communities through Education and Outreach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Research and Monitoring Track Endangered Fish Status and 

Support Adaptive Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 & 17

Expenditures

Upper Colorado River Endangered Fish Recovery Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

San Juan River Basin Recovery Implementation Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Providing Endangered Species Act Compliance for Water Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Table of Contents

Colorado Pikeminnow Humpback Chub Bonytail Razorback Sucker

Illustrations© Joseph R. Tomelleri
Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 3

Geographic Scope: 

The Upper Colorado River Endangered Fish Recovery

Program is recovering humpback chub, bonytail, Colorado

pikeminnow, and razorback sucker in the Colorado River

and its tributaries in Colorado, Utah, and Wyoming. The

Recovery Program was initiated in 1988 with the signing of

a cooperative agreement by the Governors of Colorado,

Utah, and Wyoming; the Secretary of the Interior; and the

Administrator of Western Area Power Administration. In

2001, these parties agreed to extend the cooperative agreement through September 30, 2013.

Recovering Endangered Fishes in the Upper Colorado and 

San Juan River Basins

The Intermountain West is the nation’s fastest-growing region and a critically important energy-producing area of the country.

Recovery Program partners recognize that their collaborative conservation partnership provides the most workable approach to 

recover endangered species while meeting growth-induced energy and water demands. The recovery programs are working to 

recover endangered fishes that live in the Colorado River Basin and nowhere else in the world.

The San Juan River Basin Recovery Implementation

Program is recovering Colorado pikeminnow and razorback

sucker in the San Juan River and its tributaries in Colorado,

New Mexico, and Utah. The Recovery Program was established in 1992 with the signing of a cooperative agreement

by the Governors of Colorado and New Mexico; the

Secretary of the Interior; the Bureau of Indian Affairs, the

Southern Ute Indian Tribe, the Ute Mountain Ute Indian

Tribe, and the Jicarilla Apache Nation. The Bureau of Land

Management and the Navajo Nation joined the program in

1992 and 1996, respectively. The parties extended the cooperative agreement through 2023.
4 2006-2007 Program Highlights

Upper Colorado River Endangered Fish 

Recovery Program 

◆ State of Colorado

◆ State of Utah

◆ State of Wyoming

◆ Bureau of Reclamation

◆ Colorado River Energy Distributors Association

◆ Colorado Water Congress

◆ National Park Service

◆ The Nature Conservancy

◆ U.S. Fish and Wildlife Service

◆ Utah Water Users Association

◆ Western Area Power Administration

◆ Western Resource Advocates

◆ Wyoming Water Association 

San Juan River Basin Recovery

Implementation Program 

◆ State of Colorado

◆ State of New Mexico 

◆ Bureau of Indian Affairs

◆ Bureau of Land Management

◆ Bureau of Reclamation

◆ Jicarilla Apache Nation

◆ Navajo Nation

◆ Southern Ute Indian Tribe

◆ Ute Mountain Ute Tribe

◆ U.S. Fish and Wildlife Service

◆ Water Development Interests

Partners’ Active Commitment and Participation

Key to Recovery Programs’ Success

Given the Colorado River’s complex habitat changes

and demands on water resources, Recovery Program

partners recognize that collaboration is necessary to

accomplish the dual objectives of recovering endangered fish

species while providing water for human needs. Each partner

fully participates in developing and implementing management actions leading toward delisting of the endangered

Colorado River fishes. The recovery programs have earned

accolades for their management approach, their proven track

record of accomplishments, and their partners’ long-term

commitments of staff, time, and money. 

Congressional support and continued funding of agency

involvement and program construction projects demonstrate

the effectiveness of these public/private conservation partnerships. The recovery programs’ success is a direct result of the

active commitment and participation of their partners:
NEW MEXICO

“Congress enacted Public Law 106-392 with strong bipartisan support. Public Law 106-392 authorizes the federal

government to provide up to $46 million of cost sharing for

the implementation of capital projects... The four participating states of New Mexico, Colorado, Utah and Wyoming

and their water users will contribute up to an aggregate of

$17 million to the programs, and $17 million will be contributed from revenues derived from the sale of Colorado

River Storage Project hydroelectric power....The substantial non-federal cost sharing funds demonstrate the strong

commitment and effective partnerships that are present in

both the San Juan and Upper Basin programs.”

Bill Richardson, Governor, State of New Mexico

UTAH

“The Recovery Program is a mutually supported partnership involving the states of Utah, Colorado, New Mexico

and Wyoming, as well as environmental organizations,

power users, water users and development interests. It is

important to note that, because of the cooperation between

the partners, water development along the river has continued to proceed without a single lawsuit.”

Jon M. Huntsman, Jr., Governor, State of Utah

WYOMING

“These recovery programs have become national models for

collaboratively working to recover endangered species while

meeting water use and water development demands in compliance with the Endangered Species Act, state law, and

interstate compacts in the Upper Colorado River Basin

region of the Intermountain West.”

Dave Freudenthal, Governor, State of Wyoming

Demonstrated Achievements Draw Bipartisan

Support for Endangered Fish Recovery Programs

The recovery programs have become national models,

demonstrating that public/private partnerships can

effectively recover endangered species and resolve

Endangered Species Act-related conflicts. State and federal

leaders (including the Congress) continue to provide bipartisan

and critically important support and funding for these programs

in recognition of their proven effectiveness.

DEPARTMENT OF THE INTERIOR

“Faced with the need to manage the [Colorado] river for

threatened and endangered fish and other wildlife, the Fish

and Wildlife Service, the Bureau of Reclamation and many

other partners developed the Upper Colorado River

Endangered Fish Recovery Program, the Lower Colorado

Basin Multi-species Conservation Program, and the San

Juan River Basin Recovery Implementation Program.

As a result we are making progress toward recovery of

endangered fish, while addressing the demand for water

development to support growing western communities.

For example, in the Upper Colorado River Basin, the Fish

and Wildlife Service has now consulted on nearly 1,400

water projects, using the Recovery Program as a reasonable

and prudent alternative under the Endangered Species Act.

This allows these projects to go forward while ensuring the

conservation of the fish.”

Secretary of the Interior Dirk Kempthorne, Dec. 15, 2006 

Colorado River Water Users Association Annual Meeting 

Las Vegas, Nevada

“Although the Fish and Wildlife Service is legally mandated

to conserve species protected under the Endangered Species

Act, we can’t do it alone. We know that success requires the

power of effective partnerships -- from state and federal personnel to non-governmental organizations. The Upper

Colorado River and San Juan River Basin recovery programs

have succeeded in bringing stakeholders together, uniting

conservation efforts, and striking the necessary balance

between species conservation and human needs.”

U.S. Fish and Wildlife Service Director Dale Hall

Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 5
6 2006-2007 Program Highlights

Federal Laws Authorize Cost-Sharing and Show

Congressional Commitment to Species Recovery

While Congressional authorization to fund capital

construction projects and operation and maintenance has been enacted in federal law, the Upper

Colorado River and San Juan River Basin recovery programs’

continued success depends on obtaining sufficient funding to

implement recovery actions. Current federal laws authorize

funding for capital construction projects and operation and

maintenance. 

CAPITAL FUNDING

Public Law 106-392, signed into law on October 30, 2000,

authorizes the Bureau of Reclamation to provide cost-sharing

for capital construction projects for both recovery programs.

P.L. 107-375 (2002) extended the authorization period to

complete capital construction projects to 2008. P.L. 109-183

(2006) authorized an additional $15 million for capital construction for the Upper Colorado River program and extended the capital construction period to 2010 for both programs.

Construction funding is capped at $126 million: 

$108 million for the Upper Colorado River program and 

$18 million for the San Juan River Basin program.

Colorado River Storage Project (CRSP) power customers,

water users, and the States of Colorado, New Mexico, Utah,

and Wyoming provide non-federal cost-sharing funds. 

Power Revenues

The Secretary of Energy, acting through the Western Area

Power Administration, is authorized to expend up to $17 million of CRSP power revenues for capital projects construction.

These revenues are treated as a non-federal contribution, but

are reimbursable costs assigned to power for repayment under

Section 5 of the CRSP Act. 

States Demonstrate their Commitment by 

Cost-Sharing Capital Projects

The four participating states are collectively contributing

$17 million. 

The states’ contributions are funded through several unique

and creative means:

◆ Colorado’s legislature created a Native Species

Conservation Trust Fund in 2000 through which an annual

“Species Conservation Eligibility List,” submitted by the

Department of Natural Resources, is funded by a joint resolution of the State’s General Assembly. 

◆ New Mexico’s legislature appropriated funds to meet the

state’s cost-share contributions to capital recovery projects in

the San Juan River Basin. 

◆ Utah’s legislature created a Species Protection Account

within the General Fund in 1997 which receives Brine

Shrimp Royalty Act-created revenue. In 2000, Utah dedicated 1/16th of one cent of its general sales tax to water development projects and directed funding to the Upper Colorado

River program. 

◆ Wyoming’s legislature appropriated its funding share 

during its 1998 and 1999 sessions.

BASE (O&M) FUNDING

P.L. 106-392 also provides up to $6 million per year (adjusted

annually for inflation) of CRSP power revenues for base (noncapital) funding for the two programs. This provides up to 

$4 million for the Upper Colorado River program and up to

$2 million for the San Juan River Basin program. After 2011,

power revenues may be used only for monitoring and to operate and maintain capital projects. The states also contribute

about $350,000 per year to base funding through in-kind services

or agency cash contributions.

Colorado $9.146 M $8.065 M $1.081 M

New Mexico 2.744 M 0.000 M 2.744 M

Utah 3.422 M 3.422 M 0.000 M

Wyoming 1.688 M 1.688 M 0.000 M

Total $17.000 M $13.175 M $3.825 M

Upper Colorado 

River Rec. Program

San Juan 

Rec. Program

Capital Project Cost-Sharing by the States

Capital Construction Cost-Sharing for Upper

Colorado and San Juan Programs

Upper Colo. Rec. Program . . . . . . . . . . . . . . . . .$108 million

San Juan Recovery Program . . . . . . . . . . . . . . . . .$18 million

Total . . . . . . . . .$126 million

Sources of Revenue

Federal Non-Federal

Congress: $61 million Power Revenues: $17 million

States: $17 million

Water and Power: $31 million

Total: $65 million 
Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 7

Recovery Programs Rely on Recovery Goals 

to Manage Actions and Measure Success

The recovery programs rely on recovery goals as the

foundation documents to develop and implement

management actions and measure success as they

work to recover the endangered humpback chub, bonytail,

Colorado pikeminnow, and razorback sucker. The recovery

goals provide objective, measurable criteria for downlisting to

“threatened” and delisting (removal from Endangered Species

Act [ESA] protection).

Recovery is based on reduction of threats and improvement of

a species status during the time it is listed under the ESA.

Recovery goals identify the number and age of fish that comprise a specified number of self-sustaining wild populations.

They also identify site-specific management actions that

reduce threats to the species associated with the ESA’s five

listing factors. 

The U.S. Fish and Wildlife Service will consider downlisting

or delisting the endangered fishes once the required demographic and genetic standards for self-sustaining populations

are reached and the necessary management actions are

achieved to reduce the threats that caused them to be listed.

The Service approved the initial recovery goals on August 1,

2002, with the requirement that they be reviewed and updated at least once every 5 years to include any new information.

This review is underway with completion slated for early

2008. Results will be available for public review and comment

in the Federal Register.

Actions to Recover the Fishes

The recovery programs implement management actions within five major program elements. They primarily address

threats associated with present or threatened destruction,

modification, or curtailment of habitat or range (ESA listing

factor A) disease or predation (ESA listing factor C). 

The five program elements are:

◆ Habitat Management – Identify and provide adequate

instream flows.

◆ Habitat Development – Restore habitat to develop

spawning and nursery sites, provide fish passage at dams,

maintain water quality, and prevent fish from being trapped in

diversion canals.

◆ Nonnative Species and Sportfishing – Reduce the

threat of certain nonnative fish species while maintaining

sportfishing opportunities. 

◆ Endangered Fish Propagation and Stocking – Produce

genetically diverse fish in hatcheries and stock them in the

river system. 

◆ Research, Monitoring, and Data Management –

Provide data on life-history requirements of the endangered

fishes and monitor populations to measure progress toward

achieving the recovery goals.

Highlights of recent accomplishments to recover the fishes are

described on the following pages for each program element.

Endangered Species Act Listing Factors

A. Present or threatened destruction, 

modification, or curtailment of habitat or 

range.

B. Overutilization for commercial, recreational, 

scientific, or educational purposes.

C. Disease or predation.

D. Inadequacy of existing regulatory 

mechanisms.

E. Other natural or manmade factors affecting 

continued existence.

The Recovery Program worked with the Audubon Society to restore a 26-acre

floodplain wetland at the Lucy Ferril Ela Wildlife Sanctuary in western Colorado.
8 2006-2007 Program Highlights

Implementing Innovative Solutions to

Manage Water and Improve River Habitat

The recovery programs implement innovative solutions to meet the water needs of growing western

communities while providing adequate instream

flows to restore river and floodplain habitat to benefit endangered fishes. The recovery programs’ partners cooperatively

manage water resources in accordance with state water law,

individual water rights, and interstate compacts. This is

accomplished through a variety of means including: leases and

contracts for water supplies; coordinated water releases from

upstream reservoirs; efficiency improvements to irrigation systems to reduce water diversions; and re-operation of federal

dams and reservoirs. These water-management actions benefit

recreational, municipal, and agricultural water users, as well as

the endangered fishes.

The Bureau of Reclamation’s administrative actions in 2006 to

change operations at Flaming Gorge and Navajo dams to help

meet flow recommendations for the endangered fishes were

landmark events for both recovery programs.

“The re-operation of Navajo and Flaming Gorge dams to

create river conditions more hospitable to native fish, while

meeting the projects’ other purposes, is a significant and 

important step in the process of recovery and, ultimately, the

delisting of these endangered species.”

Dan Luecke, Western Resource Advocates

◆ Coordinated reservoir operations in the Colorado River

allow upstream reservoir owners to voluntarily release water to

enhance river spring peak flows and improve fish habitat

Upper Colorado River Endangered 

Fish Recovery Program

without affecting those reservoirs’ yields. In 2006, a total of

28,460 acre-feet of water was released, which added an average of 1,800 cubic-feet-per-second to the annual peak flows.

This was the first year since 1999 that runoff conditions

enabled coordinated reservoir operations to occur. 

◆ Releases from upstream Colorado River reservoirs to

enhance summer base flows and improve endangered fish

habitat began in 1990. From 1990 through 1999, about

19,000 acre-feet of water per year was released. With the completion of a programmatic biological opinion in December

1999, releases increased to about 48,000 acre-feet on average

per year. Contributing to this increase is water conserved by

improvements to the Grand Valley Project canal system in

western Colorado which has reduced water diversions by 10

to 16 percent while meeting irrigation demands. 

San Juan River Basin Recovery

Implementation Program

◆ Water shortage-sharing agreements among local water

users, American Indian Tribes, and state and federal agencies

help ensure that water is shared in times of shortage among

human uses and endangered fish needs. Navajo Reservoir

releases have been reduced to conserve water during winter

and provide more water in the spring and summer.

◆ Hydrology modeling is a tool used to assess the effects of

changing water storage and releases to benefit fish habitat while

not impacting water contractors’ uses. Testing of the Third

Generation San Juan River Recovery Implementation Program

Hydrology Model is scheduled for completion in 2007. 

Flaming Gorge Dam on the Green River is operated to help meet flow and 

temperature recommendations to benefit endangered fish.

Navajo Dam is operated to help meet flow recommendations for the San Juan River.
Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 9

Cooperative Effort to Enlarge Colorado’s Elkhead

Reservoir Benefits People and Endangered Fish

The Upper Colorado River Endangered Fish Recovery

Program saw an important milestone in 2006 with

the completion of the Elkhead Dam and Reservoir

Enlargement Project in northwest Colorado. The project provides additional storage capacity both to augment flows in the

Yampa River and for human use in the Yampa River Basin.

The Recovery Program partnered with the Colorado River

Water Conservation District (River District) and other state

and local agencies on a 13,000 acre-foot enlargement of

Elkhead Reservoir. The Recovery Program funded $13.2 million of the $31 million project. The River District funded the

remaining $17.8 million.

The dam enlargement is a unique example of water development and environmental interests working together to

achieve common goals. This type of proactive action avoids

conflicts between water users and fish recovery actions and

ensures that the Recovery Program is conducted in accordance with state water law and interstate compacts.

Razorback suckers and Colorado pikeminnows spawn in the

lower reaches of Yampa Canyon, which also harbors one of

five remaining populations of humpback chub in the Upper

Colorado River Basin.

“The Yampa River plays a critical role in the lifecycle of the

endangered fishes,” said Recovery Program Director Bob

Muth. “The cooperation that led to completion of the

Elkhead Reservoir enlargement reflects the spirit of the

Recovery Program. The enlargement ensures that water is

available to release into the Yampa River to augment latesummer flows and benefit the endangered fishes.”

On the human side of the equation, some 5,000 acre-feet of

water is newly available for future growth in Moffat County.

The project also creates an improved recreational amenity for

the people of Routt and Moffat counties. Colorado State

Parks and the City of Craig will build improved camping, dayuse and boating facilities this spring alongside the reservoir.

The reservoir also serves as a repository for nonnative sportfish removed from the Yampa River and a revitalized attraction for anglers.

“At the risk of overusing the word, the cooperation behind

this project cannot be overemphasized,” said River District

Project Engineer Ray Tenney. “Cooperation got us to the construction phase at which point the contractor, the on-site

engineer, local governments, and the Recovery Program all

worked together and cooperated at very high levels. Now

that the dam is completed, it will take new cooperative

efforts to operate the reservoir and protect flows for the

endangered fish and to manage the nonnative fish species to

achieve Recovery Program goals.” After the reservoir fills in early 2007, up to 5,000 acre-feet of permanent water

and 2,000 acre-feet of leased water will be available each year to augment

flows for endangered fish in the Yampa River during middle and late summer.

A new tower contains four levels of outlets to regulate dam releases. Fish

screens will prevent the escapement of nonnative sportfish from the reservoir

and into the Yampa River.
Construction Projects to Improve River

Habitat Nearly Complete

The recovery programs are working cooperatively with

American Indian Tribes, water and power customers,

and local landowners to improve fish habitat.

Congress authorized capital construction to be completed by

September 30, 2010. The programs are working to meet that

schedule.

Upper Colorado River Endangered 

Fish Recovery Program

◆ Fish passages and screens are in place at major diversion dams and canals in western Colorado. The Redlands

Diversion Dam on the Gunnison River, the Grand Valley

Irrigation Company and the Grand Valley Project Diversion

Dams on the Colorado River no longer impede fish migration

or present the risk of entrapment in canals.

◆ Price-Stubb Diversion Dam fish passage construction

on the Colorado River near Grand Junction is slated to begin

in March 2007 and become operational in April 2008. Once

this last barrier to fish migration is removed, endangered fish

will have access to an additional 50 miles of critical habitat

that has been blocked for nearly 100 years.

◆ Grand Valley Project fish passage trial operations in

2005 and 2006, allowed 1 razorback sucker, 3 humpback chubs,

and about 14,000 other native fish to move upstream. Full-time

operation of this fish passage will begin when the Price-Stubb

fish passage is completed.

◆ Redlands Diversion Dam fish passage restored access

to 50 miles of Gunnison River critical habitat for endangered fishes when completed in 1996. To date, 81 Colorado

pikeminnows, 20 razorback suckers, 1 bonytail, and over

80,000 other native fish have used the passage. Colorado

Continued on page 11

pikeminnow and razorback sucker reproduction has been

recently documented in reaches upstream of the fish passage. 

◆ Tusher Wash Diversion Dam canal fish screen on the

Green River in eastern Utah is scheduled to be constructed in

2009. Once this structure is completed, all major diversion

canals identified in the recovery goals for the upper Colorado

River system will be screened.

◆ Floodplain habitats are being made accessible to all life

stages of endangered fish by breaching or removing natural or

man-made levees. Green River research studies in 2004-2006

documented transport of razorback sucker larvae into floodplain

wetlands that serve as nursery habitat. Research continues to

identify other floodplain site modifications and to evaluate flow

and temperature recommendations for the Green River. 

Biologists released 3 million beads into the Green River to simulate drifting 

larvae and learn how they move from the river into floodplain wetlands.

Recovery Program Capital Construction

Projects in Western Colorado

These research studies clearly demonstrate the cooperation of

Recovery Program partners, including the Bureau of

Reclamation, Utah Division of Wildlife Resources, Ouray

National Fish Hatchery, Colorado State University’s Larval

Fish Laboratory, Argonne National Laboratory, and the U.S.

Geological Survey.

10 2006-2007 Program Highlights
San Juan River Basin Recovery

Implementation Program

◆ Fish access has been restored to an additional 36 miles of

critical habitat on the San Juan River with the construction

of passages at the Public Service Company of New Mexico

(PNM) weir and the Hogback Diversion Dam, and removal of

the Cudei Diversion Dam.

◆ PNM fish passage operated by the Navajo Nation has

allowed 18 razorback suckers, 26 Colorado pikeminnows, and

nearly 65,000 other native fish to use the passage since 2003. 

◆ Hogback Diversion Dam canal fish screen construction is

scheduled for completion in 2008.

◆ Arizona Public Service Company weir fish passage

designs are being developed and evaluated with construction

scheduled to begin in October 2008.

◆ Fruitland Diversion Dam’s rock weir may be replaced by

a more permanent structure pending the outcome of a Bureau

of Reclamation feasibility study. A new structure would eliminate the need for annual instream work to rebuild the rock weir

after high flows, benefiting fish habitat and water-user operations. 

The Navajo Nation operates the fish passage at the Public Service Company of

New Mexico weir.

The Recovery Program has restored endangered fish access to critical habitat on

the San Juan River upstream of the Cudei Diversion Dam.

Recovery Program Capital Construction

Projects in the San Juan River Basin

Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 11
Reestablishing Fish Populations through

Propagation and Stocking

Hatchery-produced, stocked fish form the foundation

to reestablish naturally self-sustaining populations

of razorback sucker and bonytail in the upper

Colorado River system and razorback sucker and Colorado

pikeminnow in the San Juan River. The recovery programs’

maximize the genetic diversity of wild broodstocks used to

produce fish in hatcheries to increase the likelihood that

stocked fish can cope with local habitats. Both recovery programs implemented new stocking plans in 2003 to expedite

reestablishment of wild populations. The recovery programs

fund six hatchery facilities to produce the fish necessary to

meet the stocking targets. The Grand Valley Endangered Fish

Facility, Dexter National Fish Hatchery and Technology

Center, Uvalde National Fish Hatchery, and Ouray National

Fish Hatchery produce razorback suckers. Dexter, the State of

Colorado’s J.W. Mumma Native Aquatic Species Restoration

Facility, and the State of Utah’s Wahweap Fish Hatchery produce bonytails. Dexter also produces Colorado pikeminnows.

Grand Valley Endangered Fish

Facility, Grand Junction, CO

J.W. Mumma Native Aquatic Species

Restoration Facility, Alamosa, CO

Dexter National Fish Hatchery &

Technology Center, Dexter, NM

Uvalde National Fish Hatchery,

Uvalde, TX

Ouray National Fish Hatchery,

Vernal, UT

Wahweap State Fish Hatchery, 

Big Water, UT

Fish Stocked in 2005 and 2006 to Meet Annual River Stocking Targets

Species River Annual River Target Fish Stocked 2005 Fish Stocked 2006

Colorado pikeminnow . . . . . . . . . . . San Juan . . . . . . . . . . . . . . . 303,000 . . . . . . . . . . . . . . 306,800 . . . . . . . . . . . . . . 326,547

Razorback sucker . . . . . . . . . . . . . . . San Juan . . . . . . . . . . . . . . . 11,400 . . . . . . . . . . . . . . . 1,996a . . . . . . . . . . . . . . . 18,793

Colorado and Gunnison . . . . 9,930 . . . . . . . . . . . . . . . . 11,633 . . . . . . . . . . . . . . . 11,559

Middle Green . . . . . . . . . . . . 9,930 . . . . . . . . . . . . . . . . 4,878a . . . . . . . . . . . . . . . 10,091

Lower Green . . . . . . . . . . . . . 9,930 . . . . . . . . . . . . . . . . 4,243a . . . . . . . . . . . . . . . 10,313

Bonytail . . . . . . . . . . . . . . . . . . . . . . Colorado . . . . . . . . . . . . . . . . 5,330 . . . . . . . . . . . . . . . . 6,067 . . . . . . . . . . . . . . . . 5,554

Middle Green . . . . . . . . . . . . 5,330 . . . . . . . . . . . . . . . . 5,980 . . . . . . . . . . . . . . . . 5,045

Lower Green . . . . . . . . . . . . . 5,330 . . . . . . . . . . . . . . . . 3,100b . . . . . . . . . . . . . . . 3,270b

a Problems with predation and other factors affecting survival of fish in grow-out ponds in 2005 were corrected in 2006. 

b Distribution of stocked fish to meet the annual river targets will change beginning in 2007.

12 2006-2007 Program Highlights
Results of stocking efforts are successful in reestablishing endangered fish populations throughout the

Upper Colorado River and San Juan River basins.

The recovery programs continue to monitor survival and

reproduction of stocked fish to evaluate and improve stocking

strategies.

RAZORBACK SUCKER

◆ About 2,550 recaptures of stocked razorback suckers

were reported from the Green, Colorado, and Gunnison rivers

in 2000-2005. Some fish were recaptured 4 years after stocking.

◆ Stocked razorback suckers are moving between the

Green, Colorado, and Gunnison rivers. This exchange of

individuals between rivers suggests that razorback suckers may

eventually form a network of populations or subpopulations.

◆ Stocked razorback suckers are behaving as wild fish.

They have been recaptured or observed in reproductive condition at spawning sites in the Green and San Juan rivers.

◆ Stocked razorback suckers are reproducing in the Green,

Gunnison, Colorado, and San Juan rivers based on captures of

larval fish.

◆ Razorback sucker larvae are surviving through the

first year in the Green, Gunnison, and San Juan rivers based

on captures of juveniles.

COLORADO PIKEMINNOW

◆ About 8,400 recaptures of stocked Colorado

pikeminnows were reported from the San Juan River in 2004-

2006. Numbers of recaptures in 2005 and 2006 were higher

than in previous years.

◆ Recaptures indicate that stocked fish are surviving, with

many fish approaching adulthood. Biologists anticipate 

documenting natural reproduction through the collection of

larvae in future years.

BONYTAIL

◆ Over 44,000 subadult or adult bonytails have been

stocked since implementing the new stocking plan in 2003.

◆ About 200 stocked bonytails were recaptured in 2004-

2005, all within 1 year after stocking. The Upper Colorado

River program is investigating ways to modify the stocking

plan to improve bonytail survival.

Stocking Efforts Show Encouraging Results

About 1,900 recaptures of stocked razorback suckers were reported from the San

Juan River since 2000. Numbers of recaptures in 2005 and 2006 were higher than

in previous years. Some fish were recaptured 13 years after stocking in the San

Juan River.

Biologists tag Colorado pikeminnows before stocking them in the San Juan River.

More than 1 million juvenile or subadult fish have been stocked since 2002.

Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 13
Developing Solutions to Manage Nonnative

Fishes and Provide Sportfishing Opportunities

Upper Colorado River Endangered Fish 

Recovery Program

◆ Active removal beginning in 2002 has reduced the abundance of nonnative northern pike in the Green River, Utah,

to a consistently low level.

◆ An innovative study is underway to identify the source

of nonnative smallmouth bass in rivers of western Colorado

through analysis of fish otoliths (ear bones). Otoliths have

growth layers (like tree rings) whose chemistry reveals clues

about where a fish lived during specific times of its life. This

information will help determine the most cost-effective and

efficient management methods.

San Juan River Basin Recovery 

Implementation Program

◆ Active removal since 2001 has reduced the abundance

of nonnative channel catfish. Today, the population appears

to be dominated by juvenile fish, thereby reducing the potential for both channel catfish reproduction and predation on

large native fish.

◆ Recreational fishing opportunities are enhanced at area

lakes through relocation of channel catfish coordinated with

the Navajo Nation and the State of New Mexico.

◆ Active removal beginning in 2001 has reduced the abundance of nonnative common carp to a level where, in 2006, collections of Colorado pikeminnows outnumbered common carp.

Predation or competition by nonnative fish species is a serious threat to the endangered fishes and perhaps the most challenging to manage. The recovery programs are proactively working hard to meet the challenge of nonnative fish management by removing the most problematic nonnative fishes from rivers, and preventing nonnative fish from entering the

river system in areas inhabited by endangered fish. The actions recognize the dual responsibilities of state and federal wildlife

agencies to conserve native fish species while providing sportfishing opportunities.

Biologists are encouraged

that they are seeing fewer

channel catfish of this size

during nonnative fish

management efforts.

This children’s fishing pond in Craig, Colorado, is one of several locations where

biologists are placing smallmouth bass that are removed during nonnative fish

management efforts on the Yampa River.

Declines in Adult Common Carp Catch

Rates in the San Juan River

30

20

10

0

2001 2002 2003 2004 2005 2006

14 2006-2007 Program Highlights

Numbers of Northern Pike Captured in the

Green River, Utah, 1996-2006*

300

250

200

150

100

50

0

1996

1997

1998

1999

2001

2002

2003

2004

2005

2006

* Sampling did not occur in 2000.
Involving Communities through

Education and Outreach

Recovery Program Web Sites

Upper Colorado River:

ColoradoRiverRecovery.fws.gov

San Juan River: southwest.fws.gov/sjrip

The recovery programs work proactively to increase

public awareness of, and support for, endangered fish

recovery. The recovery programs invite full public

participation and understanding of program activities through

the conduct of public meetings and the distribution of a wide

range of educational materials, including newsletters, fact

sheets and reports such as Program Highlights.

Key outreach efforts, previously conducted separately by the

two recovery programs, have been integrated to ensure 

delivery of accurate and consistent messages and achieve cost

savings. Local communities help promote awareness of the

endangered fishes and their recovery in a variety of ways.

◆ A new interpretive exhibit opened in 2006 featuring an

aquarium with endangered fish at Glen Canyon Dam’s Carl

Hayden Visitor Center in Page, Arizona. The recovery programs jointly partnered with state, federal, and Colorado

River Storage Project power customers.

◆ The recovery programs provide information at major

water conferences in Colorado, Nevada, Utah, and Wyoming.

◆ Fifth-grade classrooms established aquariums with

endangered fish at a dozen schools in western Colorado.

Students care for the fish during the school year and help tag

and release them into the river.

◆ The fish passage at the Public Service Company of

New Mexico weir continues to provide educational opportunities to students from local schools, the Shiprock Boys

and Girls Club, and the local Headstart Program.

◆ The Grand Valley Audubon Society installed interpretive signs at a restored floodplain wetland at the Audubon’s

Lucy Ferril Ela Wildlife Sanctuary in Grand Junction,

Colorado.

Local students learn to identify native and nonnative fishes by helping 

biologists sort the day’s catch at the fish passage at the Public Service Company

of New Mexico weir on the San Juan River.

This Grand Valley Audubon Society wetland historically provided important

nursery habitat for razorback suckers.

The Center’s 360,000 annual visitors learn about endangered fish.

Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 15
Research and Monitoring Track Endangered Fish

Status and Support Adaptive Management

The recovery programs monitor reproduction, growth, survival, and abundance of endangered fish in the wild. Results are

used to track progress toward achieving the recovery goals, assess the effectiveness of management actions, and adjust

recovery efforts through adaptive management.

Downward trends in some humpback chub and Colorado pikeminnow populations and increased abundance of problematic nonnative fishes have been observed during dry weather and low river runoff conditions since 1999. The recovery programs are

actively implementing management actions to reduce these impacts.

HUMPBACK CHUB

◆ Five humpback chub populations inhabit canyonbound river reaches of the Upper Colorado River Basin.

• About 3,000 adults occur in Black Rocks and

Westwater canyons, and the population in Desolation/Gray

canyons is about 1,000 adults.

• Populations in Yampa and Cataract canyons are small,

each consisting of a few hundred adults.

BONYTAIL

◆ Stocking continues to reestablish bonytail populations in the upper basin. Stocking expanded into floodplain

wetlands to enhance growth and survival of the species (see

pages 12-13).

◆ Stocked bonytails being recaptured in several locations throughout the Green and Colorado rivers, provide additional information about life-history and habitat requirements.

Utah’s Wahweap Fish Hatchery produces and stocks bonytails to establish populations. Stocked bonytails are being recaptured in the Green and Colorado rivers.

Researchers sample for humpback chubs in Black Rocks, a canyon in western

Colorado, to estimate the abundance of this population.

Bonytails raised in hatchery ponds at Utah’s Wahweap Fish Hatchery are 

prepared for transport to the river.

Continued on page 17

16 2006-2007 Program Highlights

The largest humpback chub population in the upper basin lives in Westwater

Canyon in Utah where this fish was captured.
COLORADO PIKEMINNOW

◆ Wild Colorado pikeminnow populations occur in the

Colorado and Green river systems of the Upper Colorado

River Basin:

• Abundance of adults in the Colorado River system has

generally increased since 1992 (see chart at right).

• Abundance of adults in the Green River system

declined from 3,100 to 2,300 in 2001-2003. Collections of larvae in 2006 indicate a strong reproductive year. Monitoring of

year-classes provides insight on reasons for the downward population trends and guides actions to reverse these trends.

RAZORBACK SUCKER

◆ Razorback sucker populations show success as

stocked fish survive and reproduce (see pages 12-13).

• Stocked razorback suckers in the Green and San Juan

rivers have been captured at spawning sites in reproductive

condition, and captures of young fish in the Green, Gunnison,

Colorado, and San Juan rivers demonstrate that these fish are

reproducing.

◆ Stocking efforts continue in the San Juan River to

achieve recovery goals (see pages 12-13).

• Before stocking began, an estimated 19 wild adult fish

remained in the San Juan River.

• The U.S. Fish and Wildlife Service concluded in 2005

that Colorado pikeminnow and razorback sucker populations

in the San Juan River are more secure today than during the

1980s and 1990s, and the threat of extinction has been

reduced.

This female Colorado pikeminnow (37 in., 16.8 lbs) used the Redlands Diversion

Dam fish passage on the Gunnison River in 2002.

This razorback sucker used the Public Service Company of New Mexico weir fish

passage on the San Juan River.

Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 17

Stocking razorback suckers to reestablish a population in the Green River system.

Photo courtesy of Tom Ross, Steamboat Pilot & Today

Trend in Abundance of Adult Colorado Pikeminnows in the 

Colorado River, 1992-2005

1200

1000

800

600

400

200

0

92 94 96 98 00 02 04 06
Expenditures

Upper Colorado River Endangered Fish Recovery Program

Total Partner Contributions = $174,509,300 (FY 1989-2007)

Water Users

$2,224,160

FY 88 Appropriation

$973,000

Utah

$5,047,300

Wyoming

$1,683,600

Nonnative 

Fish Management

14%

Information, Education 

and Public Involvement

1%

Research and Monitoring

10%

Propagation 

and Genetics 

Management

12%

Habitat Restoration

31%

Program 

Management

14%

Instream Flow 

Identification and

Protection

14%

* (Includes Reclamation capital 

appropriation of $20,979,700 under 

ESA authorization prior to FY 1999.

** (Includes both annual and capital project

funding.)

Bureau of Reclamation: capital cost of

Ruedi Reservoir fish water releases 

(beginning in FY 03)

$3,675,000

Partners Contributions

(FY 1989-2007)

Projected Expenditures

by Category

(FY 2007 only)

Power Revenues

$64,179,200**

Bureau of Reclamation 

(capital)

$59,263,700*

Colorado

$16,115,700

U.S. Fish & 

Wildlife Service

$21,327,600

Capital Projects

Management

4%

18 2006-2007 Program Highlights
Expenditures

San Juan River Basin Recovery Implementation Program

Total Partner Contributions = $37,008,197 (FY 1992-2007)

(Not including in-kind contributions)

Program

Management

9%

Nonnative Fish

Management

15%

Flow Management

and Protection

4% Propagation and

Genetics Management

23%

State of New Mexico

$961,509

Bureau of Land Management

$350,000

State of Colorado

$362,000

Southern Ute Indian Tribe

$1,065,234

Jicarilla Apache Tribe

$19,000

Research and

Monitoring

26%

Habitat

Restoration

23%

Bureau of

Indian Affairs

$6,461,000

Bureau of

Reclamation

$9,082,939

U.S. Fish & Wildlife Service

$1,761,079

Power Revenues

$16,945,436

Projected Expenditures

by Category

(FY 2007 only)

Partner Contributions

(FY 1992-2007)

Upper Colorado River Endangered Fish Recovery Program and San Juan River Basin Recovery Implementation Program 19
Providing Endangered Species Act

Compliance for Water Projects

The Upper Colorado River and San Juan River Basin

recovery programs respond to the challenge of water

management by working cooperatively with local,

state, federal, and Tribal agencies to meet the needs of people

and endangered fish. The programs’ goal is to achieve full

recovery (delisting) of the endangered fishes, not just to avoid

jeopardy (offset impacts of water project depletions) under the

Endangered Species Act (ESA). The recovery programs serve

as a vehicle for ESA compliance (reasonable and prudent

alternatives) for water development and management 

activities by all parties, including the federal government.

Responsibilities to offset water project depletion impacts do

not fall on individual projects or their proponents.

The recovery programs provide ESA compliance for more

than 1,600 water projects depleting more than 3 million acrefeet per year. This is accomplished through cooperative

efforts. No lawsuits have been filed on ESA compliance for

any of these water projects.

ESA Compliance Granted for

Ditch Bill Easements

The Upper Colorado River and San Juan

River Basin recovery programs provide ESA

compliance for 704 agricultural irrigation or

livestock ditches and reservoirs depleting nearly 440,000 acre-feet of water on national forest

lands in Colorado. The recovery programs

greatly simplified the consultations and

reduced the cost of ESA compliance for water

users, the U.S. Forest Service, and the U.S.

Fish and Wildlife Service.

20 2006-2007 Program Highlights

Upper Colorado River Endangered Fish Recovery Program

Summary of Endangered Species Act Section 7 Consultations

(1/1998 through 12/31/2006)

San Juan River Basin Recovery

Implementation Program Summary of Endangered

Species Act Section 7 Consultants

*Depletions included in historic projects.

Depletions

Number of

State Consultations Acre-feet/yr

New Mexico 18 617,216

Colorado 94 217,456

Utah 12 9,140

Total 124 843,812

Number of

State Consultations Acre-feet/yr Acre-feet.yr Acre feet/yr

Colorado 1053 1,466,375 172,825 1,639,200

Utah 65 421,868 70,248 492,116

Wyoming 127 83,498 32,264 115,762

Regional* 238 (regional) (regional) 0

Total 1,483 1,971,741 275,337 2,247,078

Historic New

Depletions Depletions Totals
Upper Colorado River Endangered 

Fish Recovery Program

Program Partners:

State of Colorado

State of Utah

State of Wyoming

Bureau of Reclamation

Colorado River Energy Distributors 

Association

Colorado Water Congress

National Park Service

The Nature Conservancy

U.S. Fish and Wildlife Service

Utah Water Users Association

Western Area Power Administration

Western Resource Advocates

Wyoming Water Association

Upper Colorado River Endangered

Fish Recovery Program

P.O. Box 25486, DFC

Denver, CO 80225

303-969-7322

303-969-7327 Fax

coloradoriverrecovery.fws.gov

San Juan River Basin Recovery 

Implementation Program

Program Partners:

State of Colorado

State of New Mexico

Bureau of Indian Affairs

Bureau of Land Management

Bureau of Reclamation

Jicarilla Apache Nation

Navajo Nation

Southern Ute Indian Tribe

Ute Mountain Ute Tribe

U.S. Fish and Wildlife Service

Water Development Interests

San Juan River Basin Recovery

Implementation Program

2105 Osuna Rd. NE

Albuquerque, NM 87113

505-761-4745

505-346-2542 Fax

http://southwest.fws.gov/sjrip