Review of Artificial Production 

 of Anadromous and Resident Fish 

in the Columbia River Basin

Part I: 

A Scientific Basis 

for Columbia River Production Programs

April 1999 

Scientific Review Team 

Independent Scientific Advisory Board 

Ernest L. Brannon James A. Lichatowich 

Kenneth P. Currens Brian E. Riddell 

Daniel Goodman Richard N. Williams 

Willis E. McConnaha, Chair 

Program Evaluation and Analysis Section 

Northwest Power Planning Council 

851 SW 6th Avenue, Suite 1100 

Portland, Oregon 97204 

 

Council Document 99-4 
Cite as: 

Brannon, Ernest L., et. al., (Currens, Kenneth P.; Goodman, Daniel; Lichatowich, James A.; 

McConnaha, Willis E.; Riddell, Brian E.; Williams, Richard N.). 1999. Review of Artificial 

Production of Anadromous and Resident Fish in the Columbia River Basin, Part I: A Scientific 

Basis for Columbia River Production Program, Northwest Power Planning Council, 139 pp. 
Scientific Review Team 

Independent Scientific Advisory Board 

April 22, 1999 

Mr. Todd Maddock, Chair 

Northwest Power Planning Council 

851 S.W. Sixth Avenue, Suite 1100 

Portland, OR 97204 

Dear Mr. Maddock: 

I am pleased to transmit to you the first phase of the Scientific Review Team's (SRT) report on 

hatchery programs in the Columbia River Basin. This version updates our December version and 

adds considerations of resident fish artificial production. 

The report includes an historical overview of artificial production within the basin, a review of the 

state of the science with respect to effectiveness of artificial production as a means to augment 

harvest, a review of the state of the science with respect to ecological and genetic effects of artificial 

production on wild spawning populations, and a set of recommendations in the form of guidelines 

that might guide policy on artificial production so as to be consistent with a sound scientific 

foundation. 

The proposed guidelines at this point are based on our review of the published science, which 

completes this phase of our task in the Review of Artificial Production. In the next phase we will 

determine whether analysis of existing monitoring data resolves any of these hypotheses more 

conclusively, in the specific context of the Columbia Basin. 

The Artificial Production Review is consistent with other recent scientific reviews that considered 

this topic (the Northwest Power Planning Council's Independent Scientific Group (ISG), 1996; the 

National Research Council (NRC), 1996; and the National Fish Hatchery Review Panel (NFHRP), 

1994). There is considerable consensus among the three previous scientific reviews and our own, 

regarding the status of the science associated with artificial production. 

We understand very well that the priorities of fisheries management have changed significantly in 

recent years, so the needs that hatcheries should serve are also changing. The ecosystem based 

management approach places artificial production in the basin in a very different role than 

employed in the recent past. In particular, the reality of increasing numbers of Endangered Species 

Act listings of anadromous and resident fish puts a much higher emphasis on wild stocks and 

naturally spawning stocks. This increases the concern over the potential for artificial production to 

cause genetic and ecological harm to such stocks. But it also raises the possibility that hatcheries 

may serve some more positive role in this era of new priorities. 

The historical track record does not reassure us that hatchery programs can respond to changing 

realities and changing scientific knowledge. We hope that ways will be found to ensure that in the 

i
future this important component of the fisheries management system will evolve more rapidly and 

constructively. Even by the standards of the old objective of simply augmenting harvest to mitigate 

for lost and impaired habitat, artificial production of anadromous salmonids in the Columbia basin 

would need careful re-evaluation because of the perceived less-than-effective return of adults. 

However, under the new ecosystem management paradigm, performance assessment of hatchery 

programs in light of the potential impacts on native fish becomes most critical. 

Other major factors besides hatcheries, including some factors that are beyond human control, surely 

are playing some role in the salmon decline. And some hatcheries have performed considerably 

better than average, contributing substantially to harvest, and maintaining runs of the hatchery stock. 

One hope in undertaking the SRT evaluation is to identify causes for the differences in performance 

between hatcheries, in order to develop recommendations for improving average hatchery 

performance, as well as to add to our understanding of how hatcheries should fit into the new 

ecosystem management concept. 

There has not been adequate monitoring and evaluation of Columbia Basin salmon stocks. 

Monitoring and analysis to date has been sufficient to document rather disappointing numbers. But 

the monitoring and analysis has not been sufficient to pin down the causes of the poor performance, 

nor has it been sufficient to determine why some hatcheries perform better and some perform worse. 

The challenge in the concept of ecosystem management is how to reconcile local objectives of

providing harvest opportunities, sometimes with exotic species, with larger ecosystem objectives. 

Ecological and genetic science does provide plausible hypotheses about what some of the avoidable 

causes of poor performance might be among the anadromous salmonid hatchery fish. These 

include: inbreeding, domestication, inappropriate life history timing, inappropriate physiological and 

behavioral conditioning, over-reliance on too small a number of life history types, and exceeding 

carrying capacity in some key portions of the natural environment. Our report reviewing the science 

explains how these plausible ecological and genetic mechanisms could be operating in hatchery 

stocks. 

Given the new management emphasis on wild stocks, it is especially distressing to learn that these

mechanisms that might account for poor performance of hatchery fish could also have very negative 

effects on naturally spawning fish that interact ecologically and genetically with the hatchery 

product. Our report reviewing the science explains plausible mechanisms of interaction between the 

hatchery products and wild spawning fish. 

Ecological and genetic science suggests that artificial production must be carefully integrated into 

the functioning of the entire ecosystem. Both the ecosystem and artificial production need to be 

managed to some normative standard, in order for artificial production to be effective in meeting the 

basin's goals. Our report reviewing the science offers recommendations on how this integration and 

management might be accomplished. 

Uncertainty places a premium on experimental management to better diagnose the causes of the 

problems, and to refine the solutions. The effectiveness of experimental management depends 

critically on a comprehensive program of monitoring and analysis to detect responses to 

experiments, and to alter management according to what is learned. The programs of monitoring and 

analysis now in place in the Columbia Basin may not be equal to this task. The region, through the 

Council, needs to implement a scientifically valid, comprehensive monitoring and evaluation 

ii
program to assess hatchery procedures, production, impact on natural populations, and achievement 

of goals. 

We note, finally, our analysis under the new concept of ecosystem management in the basin must 

place hatcheries in the experimental framework, and most certainly in the perspective of ecosystem 

function we conclude that the outcomes of these experiments are not yet known. Yet artificial 

production has been implemented on a scale that will continue to commit a large percentage of the 

region's restoration resources, a large percentage of the available watersheds, and a large percentage 

of the remaining stocks to a single, unproven technology. There may be merit to reconsidering these 

priorities. 

The SRT will continue its review of hatchery programs, compilation of available data, and analysis 

of those data. We expect to finalize our review and recommendations by June 30, 1999. 

Sincerely yours, 

Willis E. McConnaha, Chair 

Scientific Review Team 

iii
Table of Contents 

I. INTRODUCTION .............................................................................................................................1 

A. SCOPE OF THE REVIEW .......................................................................................................................3 

B. DEFINITION OF ARTIFICIAL PRODUCTION..........................................................................................4 

C. RELATIONSHIP BETWEEN THIS REVIEW AND DEVELOPMENT OF THE REGIONAL MULTI-SPECIES 

FRAMEWORK ............................................................................................................................................5 

D. DEFINITION OF THE COLUMBIA BASIN ECOSYSTEM ..........................................................................6 

II. HATCHERY MANAGEMENT AND THE SALMON CRISIS ..................................................8 

III. HISTORICAL OVERVIEW OF ARTIFICIAL PRODUCTION............................................11 

A. GROWTH OF THE ARTIFICIAL PROPAGATION PROGRAM...................................................................11 

B. COMPENSATION FOR LOSS OF HABITAT ...........................................................................................17 

IV. SCIENTIFIC FOUNDATION.....................................................................................................23 

A. THE EARLY CONCEPTUAL FOUNDATION OF HATCHERIES ...............................................................24 

B. THE HATCHERY FRAMEWORK AS AN ADAPTIVE PROCESS ..................................................................28 

V. ORGANIZATION AND CLASSIFICATION OF ARTIFICIAL PRODUCTION...................37 

A. HARVEST AUGMENTATION................................................................................................................38 

B. MITIGATION......................................................................................................................................41 

C. DETERMINANTS OF PERFORMANCE..................................................................................................44 

VI. SYNTHESIS OF ARTIFICIAL PRODUCTION REVIEWS...................................................46 

A. EARLY HATCHERY EVALUATIONS .....................................................................................................46 

B. RECENT REVIEW SUMMARIES OF INDEPENDENT PANELS.................................................................51 

C. RELEVANCE OF PAST ASSESSMENTS TO THE PRESENT TASK............................................................61 

VII. IMPACTS ASSOCIATED WITH ARTIFICIAL PRODUCTION ........................................63 

A. BACKGROUND ...................................................................................................................................63 

B. RISK MANAGEMENT..........................................................................................................................64 

C. MANAGEMENT IMPACTS ON ARTIFICIAL PRODUCTION EFFECTIVENESS .........................................66 

D. GENETIC IMPACTS OF ARTIFICIAL PRODUCTION .............................................................................68 

E. ECOLOGICAL EFFECTS OF ARTIFICIAL PRODUCTION: .....................................................................76 

F. POPULATIONS AND PRODUCTION TRENDS OVER TIME.....................................................................85 

VIII. CONCLUSIONS AND GUIDELINES.....................................................................................91 

A. POINTS OF GENERAL AGREEMENT WITH RECENT REVIEWS ............................................................93 

B. GENERAL CONSIDERATIONS OF THE STATE OF THE SCIENCE AND THE TECHNOLOGY ....................94 

C. RELATION TO AN ECOLOGICAL FRAMEWORK ...................................................................................96 

D. GUIDELINES ON HATCHERY PRACTICES, ECOLOGICAL INTEGRATION AND GENETICS. ....................96 

LITERATURE CITED......................................................................................................................109 

APPENDIX .........................................................................................................................................130 

iv
Figures and Tables

Page 

FIGURES:

1 The number of juveniles of all salmon species released from hatcheries in

the Columbia River (1877-1928)........................................................................12 

2 Harvest of chinook salmon and the release of chinook salmon fry and 

fingerlings from hatcheries in the Columbia Basin (1877-1927) .......................13 

3 Five-year average of chinook harvest in the Columbia River (1866-1992) .......13 

4 Comparison of the seasonal distribution of the chinook harvest in the 

Columbia River in 1878 (A—daily catch per gill net boat) and 1919 (B—

weekly catch of 16 gill net boats and 22 traps)...................................................14 

5 Columbia River Basin state, tribal and federal hatchery locations.....................22 

6 Annual run size of pink salmon returning to hatchery and natural production 

streams in Prince William Sound, Alaska...........................................................30 

7 Percent survival of pink salmon fry released from Armin F. Koernig 

hatchery in Prince William Sound, Alaska .........................................................30 

8 Annual run size of sockeye salmon returning to Weaver Creek in British 

Columbia.............................................................................................................31 

9 Chinook salmon annual return to Sooes River, Washington, from hatchery 

and natural production ........................................................................................32 

10 Comparison of angler hours during pre-stocking (1985) and post-stocking 

(1987, 1988) periods at Sprague Lake, Washington................................ 36 

11 Comparison of rainbow trout before (1990,1991) and after stocking (1992-

1994) in Lake Roosevelt................................................................36 

12 Comparisons of angler trips on Lake Roosevelt before (1980) and after 

rainbow trout stocking...................................................................37 

13 Comparisons of economic value of Lake Roosevelt resident fishery before 

(1990) and after rainbow trout stocking program.................................. 37 

14 A comparison of Hood Canal chum salmon releases and subsequent run size ..39 

15 A comparison of hatchery releases of Puget Sound 1+ coho with subsequent 

run size................................................................................................................39 

16 Dams on the Columbia and Snake rivers............................................................86 

 17 Hatchery contribution to Columbia Basin juvenile salmonid emigration ..........87 

18 The trend in returning anadromous salmonid populations counted over 

Bonneville Dam on the Columbia River.............................................................88 

19 The trend in total return production of anadromous salmonid populations to 

the Columbia River plus commercial landings...................................................89 

20 Chinook salmon returns to the Snake River related to the years when Lower 

Snake dams were built ........................................................................................90 

TABLES: 

1 Major hatcheries that are part of the Columbia River fisheries development 

program (Mitchell Act Hatcheries).....................................................................18 

2 Major hatcheries that are part of the Lower Snake River Compensation Plan...20 

3 Major hatcheries that are part of the Willamette mitigation program ................20 

 

v
Review of Artificial Production 

of Anadromous and Resident Fish 

in the Columbia River Basin 

Part I: A Scientific Basis for Columbia River Production Programs 

I. Introduction

In July 1997, the U.S. Senate1

 directed the Northwest Power Planning Council, with the assistance of 

the Independent Scientific Advisory Board (ISAB),2 to “conduct a thorough review of all federally 

funded hatchery programs operating in the Columbia River Basin...” with the intent to ensure that 

federal dollars are spent “wisely” and “in a cost-effective manner that maximizes the benefits to the 

fish resource.” The Council is to assess the “operation, goals and principles of state, tribal and 

federal hatcheries...” with regard to the effectiveness of their role in the broader context of fisheries 

management. The Council is to recommend to Congress a set of policies that would guide the use of 

Columbia River hatcheries. 

In response to the Congressional directive, the Council consulted with the ISAB and appointed a 

Scientific Review Team (SRT) to provide an independent assessment of the basin’s artificial 

production program. The SRT includes four members of the ISAB, two additional independent 

scientists, and a scientist from the Council staff as chair of the team. The SRT will review hatchery 

programs in the basin, analyze their effectiveness in meeting mitigation responsibilities, assess their 

success in enhancing salmonid production, and evaluate their role in supplementation of natural 

salmon and steelhead runs. The SRT analysis will provide the biological basis for the Council's 

recommendations to Congress. 

To provide timely advice for the Council’s report to Congress, the SRT is conducting the analysis as 

three sequential tasks: 

 

1

 U.S. Senate Energy and Water Development Appropriation Bill, 1998, Report 105-44. 

2

 The ISAB was created jointly by the Northwest Power Planning Council and the National Marine Fisheries Service to

provide independent scientific advice regarding fish and wildlife management in the Columbia River Basin. The ISAB

consists of 11 scientists appointed with the assistance of the National Research Council. 

1
1. A summarization of current scientific knowledge on artificial production and its 

implications for Columbia River programs. 

2. A compilation of the data relating to the performance of artificial production in the 

Columbia River Basin. 

3. An analysis of this information in light of current knowledge to assess the performance of 

artificial production in the Columbia River Basin. 

This report addresses the first task, which is to provide background information on the state of the 

science that relates to artificial production in the basin. The scientific rationale developed in this 

report takes the form of guidelines that could form the basis of recommendations regarding artificial 

propagation, in the context of ecosystem management. The second task, assembling the database of 

all past and current records on artificial production in the basin, has been assigned to a contractor. 

The third task will be the analysis of hatchery programs and the database, and finalizing the report. 

Each task will be summarized in separate reports to the Council and then integrated into a final 

report. 

This paper provides the SRT’s analysis of the history of artificial production and other hatchery 

evaluations related to the Columbia basin. Hatcheries initially were used to augment the fishery, 

later to mitigate for habitat destruction by development activities, and more recently to supplement 

natural production and conserve salmon using captive brood stock techniques. These roles are 

defined and discussed in this report, and the state of current knowledge of the genetic and ecological 

effects of hatcheries is summarized, as well. 

The next phase of the SRT report, where applicable, will use guidelines associated with uncertainties 

as a basis to evaluate hatchery performance. The evaluation should identify production and 

operational strategies that can assist in development of hatchery policy. Performance evaluation will 

use production return criteria and/or fulfillment of mitigation objectives as the basis of assessment. 

The two evaluations, with recommendations emanating from both the scientific analysis and 

hatchery performance evaluation, will be articulated in a proposed conceptual foundation for the 

Columbia River Basin’s artificial production program. Whether or not this conceptual foundation is 

adopted as the basis for regional hatchery policy, it is imperative that policy is based on a scientific 

foundation and that adaptive management is pursued using performance criteria.

2
A. Scope of the Review

Artificial production has been used in the Columbia River Basin for many purposes during this 

century. Although basin hatcheries have produced resident species, such as sturgeon and rainbow 

trout, hatchery production has focused almost exclusively on anadromous salmonids -- primarily 

coho and chinook salmon and steelhead trout. 

These three species also have been the focus of sport and commercial fisheries management in the 

basin and, ironically, recovery measures, as well. Due to the ecological, economic, recreational and 

cultural importance of these species, the Council's policy recommendations must address 

anadromous salmonids primarily, but also apply to a much broader spectrum of species. 

In the Columbia River Basin, there are hatcheries for both anadromous and resident fish.3

 Many 

resident fish hatcheries in the basin, like many anadromous fish hatcheries, are intended for 

mitigation and are located upstream from Grand Coulee and Hells Canyon dams, which are complete 

barriers to anadromous fish passage. Netboy (1986) estimated that 40 percent of the original 

spawning areas for Columbia Basin salmonids had been lost because of blockage due to dams. 

Return to the River estimates a 55-percent loss (45 percent remaining; Page 353). Of the original 

salmon and steelhead habitat available in the basin, 55 percent of the watershed area and 31 percent 

of stream miles are now inaccessible to anadromous salmon, having been blocked by dam 

construction (NRC 1996, pg. 63). Furthermore, much of this inaccessible habitat was irreplaceable 

natural spawning habitat, located mainly in headwater regions of the basin. Thus, successful 

artificial production of resident fish is a necessary and crucial component to fully mitigate 

anadromous fish losses in these blocked areas. In addition, many native resident fish species are 

currently federally listed as threatened or endangered under the U.S. Endangered Species Act, based 

on their imperiled biological status. As with anadromous salmonids, numerous at-risk resident fish 

populations (e.g. bull trout, white sturgeon, and various resident salmonids) are also the focus of 

recovery measures. 

 

3

 Newsdata Corp., a Seattle-based news service on fish, wildlife and energy issues, estimates there are 148 fish

hatcheries in the Columbia River Basin, but this number does not include privately financed hatcheries. The information

is online at http://www.newsdata.com/fishweb/. 

3
The scope of our review concentrates on artificial production of anadromous salmonids in the 

Columbia Basin. However, most, if not all, of the scientific information relating to ecological 

impacts of anadromous salmonid hatcheries applies to the use of hatcheries that currently produce 

more than a dozen ecologically and economically valuable species of resident fish. Therefore, 

resident fish hatchery policy must be consistent with the principles in the conceptual foundation that 

the SRT will recommend to the Council for anadromous salmonids. In fact, because resident species 

do not have the distribution range of salmon and steelhead, and thus are not exposed to the same

risks facing anadromous salmonids over their migratory corridor, we expect that resident species will 

be very responsive to the principles guiding policy in anadromous salmonid management. 

Throughout the review, we make connections between anadromous and resident fish production with 

regard to principles and technologies. 

B. Definition of Artificial Production 

Artificial production and hatcheries are generally viewed as synonymous terms in that both refer to 

the same range of fish culture technologies, encompassing everything from releases of unfed, 

substrate-incubated fry to captive rearing of migrant juvenile salmonids on formulated diets in 

concrete raceways. The most common type of fish hatchery is a cluster of buildings and concrete 

raceways located adjacent to a tributary stream. But a hatchery also can be a gravel-lined incubation 

box in which artificially spawned eggs are incubated to enhance fish production. Or, a hatchery can 

be an engineered spawning channel that salmon enter to spawn naturally on graded substrate, where 

water flow is controlled to enhance egg-to-fry survival. Or, a hatchery even can be an earthen 

acclimation pond in which fingerlings are fed before dispersing into the natural stream on their own 

volition for rearing or migration. 

In this report, our focus is on the "standard" public hatchery design -- the cluster of buildings beside 

a tributary, with tray incubators and concrete raceway rearing systems that provide the entire 

freshwater feed and residence requirements before the fingerlings are released to migrate seaward.

Columbia River hatcheries were designed around variations of this “standard” incubation and rearing 

system. It is a system that has been used for most chinook and coho salmon, and steelhead trout, 

hatcheries over this century. 

This type of hatchery generally controls the entire freshwater juvenile life cycle, except the 

migratory passage. Adults are intercepted and spawned artificially, based on a breeding plan that 

4
varies from simply crossing multiple females with a composite of two or more males, to a breeding

matrix that maximizes the available genetic variability. Eggs are usually incubated in trays until 

hatching or to the point of emergence when yolk stores are nearly exhausted. Some form of 

substrate is often included in the incubation compartment to reduce alevin activity and prioritize 

stored energy for growth. At or before the emergence phase, the young fry are placed in troughs or

tanks for swim-up and early rearing, and then transferred to raceways for production rearing until 

they are distributed for release as smolts or presmolts to natural waters. Formulated diets are used 

throughout rearing, based on nutritional requirements, and fed as mash or graded pellets to 

accommodate the size of the fish as they grow. The system is well defined in a program to 

maximize efficiency of operations. 

Hatchery performance assessment understandably has been limited within the rather narrow 

definition of variables in facility design and operations common to such facilities. Because 

Columbia River hatcheries use the standard technology, performance differences have as much to do 

with management as with application of the technology itself. Variables such as the source of fish, 

release strategies, relative size and condition of smolts, water supplies, location of the hatchery and 

its location on the migratory corridor over the length of the river will affect performance. Therefore, 

the context of our evaluation is the relative performance of a particular class of hatcheries within the 

confines of river conditions in the Columbia Basin, under agency management responsibility. 

Consequently, our assessment will be an assessment of the policy and location as much as the 

technology involved. 

C. Relationship Between this Review and Development of the Regional Multi-Species Framework 

As this review is being undertaken, states, tribes and agencies of the federal government in the 

Pacific Northwest are collaborating on a multi-species planning process for fish and wildlife in the 

Columbia River Basin. The multi-species planning process is guided by a framework that links 

Columbia Basin fish and wildlife policy to a vision that balances the many values provided by the 

natural resources of the Columbia River and its tributaries. The multi-species framework will be

based on an ecological, conceptual foundation that recognizes that the river and its species are 

interrelated parts of a whole. 

The multi-species framework will include principles, goals and objectives that reconcile seemingly 

inconsistent and uncoordinated approaches to fish and wildlife policy in the region. These 

5
principles, goals and objectives will be expressed in a set of scientifically supportable alternatives 

for the future of the Columbia River -- especially as it relates to management of fish and wildlife 

resources.4

 As they are developed, these alternatives will be analyzed for their ecological impacts, 

based on an explicit conceptual foundation. The conceptual foundation includes a set of scientific 

principles that define the scientific context for the analysis.5

Once it is developed, the multi-species framework will provide systemwide direction and specific 

strategies for fish and wildlife programs, as well as objectives against which results can be 

evaluated. The conceptual foundation for artificial production developed in this review should be 

consistent with the set of scientific principles guiding development of the multi-species framework. 

In this sense, a conceptual foundation for artificial production is a refinement of the more general 

conceptual foundation for the multi-species framework, and serves to focus scientific principles on 

decisions about how to use artificial production. We believe that a scientifically supportable 

conceptual foundation, such as that guiding development of the multi-species framework and 

potentially refined by our assessment, should be the basis for developing future hatchery policies. 

D. Definition of the Columbia Basin Ecosystem 

Natural and cultural attributes define an ecosystem (ISG, 1999). The modern Columbia River 

ecosystem is far different than the ecosystem that existed before the encroachment of modern 

civilization -- as that ecosystem was different from the one that existed before Native Americans 

began exploiting the Columbia River fishery. Man's actions irrevocably altered the Columbia River 

ecosystem, and those impacts define the parameters for ecosystem management today. 

As major hydroelectric facilities multiplied in the Columbia River Basin, the free-flowing river 

became a series of linked reservoirs. This new environment favored species previously limited by 

higher velocities and cooler water temperatures. Predator and competitor species assumed new 

levels of abundance in the river system previously dominated by salmonids. For example, the 

northern pikeminnow (previously named the northern squawfish), a native salmon predator, 

 

4

 Ecological Work Group 1998, "An Ecological Framework for the Multi-species Planning Process." Available from

the Northwest Power Planning Council, Portland, OR., or at the Framework Project website at www.nwframework.org; 

click on Ecological Analysis. 

5 "Proposed Scientific Foundation for Development of a Regional Multi-Species Framework," Northwest Power 

Planning Council Report 98-16. Portland. 

6
increased in number -- and impact on salmonids -- as a result of the increased reservoir habitat. 

(Zimmer 1953, USFWS 1957, Thompsom 1959, Beamesderfer and Rieman 1991, Poe et al. 1991, 

Rieman et al. 1991. 

Perhaps even a more serious impact in the evolutionary sense, however, were the many exotic fish 

brought into the basin by private, state and federal entities, such as American shad, channel catfish, 

largemouth and smallmouth bass, blue gill, yellow perch, brown trout, brook trout and lake trout 

(Simpson and Wallace 1982). While many of these fish were introduced for sportfishing diversity 

before the ecological impacts were fully appreciated, and have now become an important part of the 

species selection offered the sportfishing public, they nevertheless have permanently changed the 

Columbia River ecosystem. Although most of the exotic species were introduced half a century ago, 

interactions among the various non-native and native fish species are likely to continue to evolve 

toward a new equilibrium (as yet unknown). 

 

Substantive and even drastic changes in species composition and habitat utilization have occurred 

over the last several decades. Preliminary surveys in the lower reaches of the Yakima River over the 

last half of 1996, for example, revealed that about two-thirds of the species encountered were 

exotics, and smallmouth bass represented over 60 percent of all fish intercepted (Monk 1997). 

Sampling gear tended to exclude fish larger than 10 centimeters in length, but as an index of general 

abundance, the survey demonstrated how dominant these species have become in some areas of the 

Basin. The impact of these newcomers, through competition or predation on endemic species, is 

unknown, but the success of exotic species has come at a cost to native fish. 

Major changes in the operation or configuration of the hydrosystem also will affect interactions 

among fish species. Changes that increase normative conditions, such as natural river drawdown in 

the lower Snake River or a major drawdown of John Day Dam (system configuration alternatives 

currently being studied by the National Marine Fisheries Service or the U.S. Army Corps of 

Engineers) would promote an equilibrium that favored coldwater native fish species over warmwater 

native and non-native fish species. 

This dynamic mix of native and non-native species defines the modern Columbia Basin ecosystem. 

Where anadromous species have been eliminated by barrier dams, mitigation has been in the form of

7
replacement resident fisheries, and sometimes those fisheries include exotic species. Moreover, 

resident fish hatchery programs often will not be complementary with the ecosystem management 

perspective adopted for anadromous hatchery production. Nor can mitigation in these cases 

necessarily imply that hatchery production will be temporary until natural production can sustain the 

population. In some cases resident fish populations have been established where none existed before 

and will be entirely dependent on artificial production. Thus, in some cases the concept of using 

supplementation hatcheries to rebuild naturally reproducing populations does not necessarily apply 

to resident fish .

Another difference between anadromous and resident fish hatcheries is performance measurement. 

Traditionally for anadromous programs, we have measured hatchery production success in terms of 

harvest return. This is often an inappropriate statistic in resident fish hatchery performance. More 

realistic performance goals for resident fish might include catch and release only, or simply having 

fish in the system available for viewing. Thus, for both anadromous and resident production, 

performance criteria should be matched with the fisheries management objective of the specific 

program or facility and in recognition of the community of fishes that are now in the basin. What 

constitutes the Columbia Basin ecosystem, therefore, is basic in how hatchery production is viewed, 

and why “normative” is such a key concept that accommodates the biological realities with the 

cultural and economic changes that define the present ecosystem. 

II. Hatchery Management and the Salmon Crisis

There is no doubt among fisheries managers that there is a crisis of major proportions confronting 

anadromous salmon and steelhead runs in the Pacific Northwest. This crisis is characterized by 

depleted populations especially in Oregon, Washington, Idaho and California, massive shrinking of 

the salmon's range, collapsed fisheries and large-scale protection under the federal Endangered 

Species Act, and nowhere in such proportions as the Columbia River Basin. Although the salmonid 

crisis receives a majority of scientific, managerial, and public attention in the Columbia Basin, 

inspection of the status of all Columbia Basin fish species reveals a wide array of resident fish also 

involved in crisis situations (e.g. bull trout, white sturgeon, and various native non-anadromous 

salmonids). 

8
Hatcheries play a unique role in this predicament. They have been identified as one of the causes of 

the current crisis, while at the same time they are also considered part of the solution. Many salmon 

biologists and culturists recognize this dual role of artificial propagation of anadromous and resident 

fish. These biologists and culturists resolve the apparent contradiction by declaring that the hatchery 

programs made mistakes in the past, but things are different now. 

At the present time, hatcheries consume about 40 percent of the annual budget for the Council's Fish 

and Wildlife Program (ISRP, 1997). If artificial propagation is going to consume such a large 

proportion of the tens of millions of dollars spent on salmon restoration, it is critical that there be 

specific answers to the following questions: 

1) What problems did the programs have in the past, and 

2) Specifically, how were those problems resolved?

Because of the unique dual role of hatcheries, we have to be sure that the past is really passed, and 

that hatchery fish are able to fit in the larger picture of ecosystem function that is being advocated as 

the new management paradigm. 

Anadromous and resident fish hatchery technology has continuously changed over the past 120 

years. Improvements include: 

• Better operational design, 

• Increased nutritional value of feeds, 

• Better disease treatments, 

• Development of tagging technology to allow monitoring the contribution and survival of 

hatchery-reared fish, 

• Increased control over hatchery environments such as water temperature and pathogens, and 

• Integration of life history traits and requirements and genetic principles in fish husbandry 

practices. 

In short, many of the operational problems that plagued hatchery operations in the past have been 

resolved. However, the distinction between intrinsic hatchery operations and management of 

hatcheries must be addressed separately. Included in management resolution is the effect of 

9
sustained fisheries on adult salmon of hatchery origin (Campton, 1995). It is the latter, Campton 

argues, that is the source of most genetic effects of hatcheries on wild stocks. Moreover, 

management is the major source of ecological impact of hatchery fish on wild stocks, and the subject 

of controversy regarding poor survival of artificially propagated fish. If the manner in which 

hatcheries are used is, in fact, contributing to poor performance of hatchery fish, the negative effects 

of hatcheries due to poor management decisions can be resolved by changing the philosophy and 

priorities of management (Campton, 1995). 

To determine if changes in management philosophy and priorities have corrected the past problems

of hatcheries, we have to look beyond the changes in technology that have occurred over the past 

century. Changes in philosophy are directly related to changes in fundamental assumptions that 

underlie hatchery and fisheries management. To determine if things really are different, it is critical 

to identify the fundamental assumptions that guided hatchery management in the past and compare 

them to the assumptions that guide hatchery management today. That can only be done through a 

historical analysis. Culturists who believe that "things are different now" often see little value in 

such analyses, with the result that fishery scientists have produced few analytical studies of earlier

program performance (Smith, 1994). Consequently, the specifics that would clarify past programs 

and the assumptions that guided them are not well known. Information is generally good with 

regard to hatchery operations. Hatchery population inventory, health status, feeding levels, 

condition and outplanting dates are in the archives of daily logs kept by the agencies. The missing 

detail is the rationale behind their hatchery programs. Understandably, the objective was increased 

production for harvest, but what motivated the approach is primarily anecdotal. 

As noted earlier, restoration programs that intend to produce a new future for anadromous and 

resident fish populations in the Columbia River Basin must be historically informed, because in a 

sense the past is never really abandoned. Programs and their philosophical underpinnings evolve, 

and this means "new " programs carry strands of ideas and assumptions that have their roots in the 

distant past. We cannot merely assume that hatchery programs today are detached from their 

historical roots without a review of those roots and their influence on current assumptions that drive 

the program. 

10
III. Historical Overview of Artificial Production

In this section, we explore the history of Columbia River Basin hatcheries to1960. Post-1960 

operations will be analyzed in our next report, when reliable data about individual hatcheries will be 

available. 

A. Growth of the Artificial Propagation Program 

Spencer Baird, the U. S. Fish Commissioner, set the stage for the arrival of artificial propagation in 

the Columbia basin. In a report he completed in 1875, Baird listed the threats to the continued 

productivity of Pacific salmon in the Columbia Basin -- dams, habitat change and overharvest -- and 

he recommended artificial propagation as the solution to those problems. According to Baird, an 

investment of $15,000 - $20,000 in artificial propagation would make salmon so abundant that there 

would be no need for restrictive 

regulations (Baird 1875). 

Given his scientific background, Baird’s 

endorsement of hatcheries in 1875 is 

puzzling. The first hatchery for Pacific 

salmon had been opened in the 

Sacramento River just three years earlier 

in 1872, and so the first brood of 

artificially propagated chinook salmon Typical turn-of-the-century salmon hatchery. 

had not yet returned as adults. Baird had (Dungeness River) 

no credible scientific information upon which to base his recommendation. However, the concept of 

maintaining and increasing the abundance of salmon through artificial propagation was consistent 

with the prevailing ideology. For example, the belief that hatcheries could eliminate the need for 

restrictive regulations supported the laissez-faire access to natural resources, a policy the public 

supported and the government encouraged. It’s clear Baird’s endorsement had social and political 

roots rather than scientific. From this rather inauspicious start, hatcheries quickly became the 

preferred approach to maintaining salmon production. 

The first hatchery in the Columbia Basin was a joint venture composed of private capital, largely 

from cannery operators, and expertise supplied by the U. S. Fish Commission. In 1877, Baird sent 

11
Livingston Stone to Astoria to meet with the board of directors of the Oregon and Washington Fish 

Propagating Company (OWFPC). The company had raised $31,000 to build and operate a hatchery, 

and Stone was one of the few individuals on the West Coast with experience in artificial 

propagation. (Stone 1879; Hayden 1930). Stone selected a site on the Clackamas River, built the 

hatchery building, raked the stream, and supervised initial operation. OWFPC closed the hatchery in 

1882. In 1888, it was leased to the State of Oregon and reopened (OSBFC 1888; Cobb 1930). After 

1888, there would never be another year in which the reproduction of salmon in the Columbia basin 

was entirely natural. 

By 1928, 15 hatcheries were operating in the basin and a total of 2 billion artificially propagated fry 

and fingerlings had been released into the river (Figure 1). 

Figure 1. The number of juveniles of all salmon species released from 

hatcheries in the Columbia River (1877-1928). (Cobb 1930) 

Because chinook salmon, especially the spring and summer races, made the highest quality canned 

product and brought the highest prices, fishermen targeted that species in the early fishery (Craig and 

Hacker 1940). The early hatchery program also focused exclusively on the chinook salmon (Figure 

2); however, when the abundance and harvest of chinook salmon began to decline, the fishery 

switched to other species, and that switch was mimicked by the hatchery program. Coho salmon and 

steelhead were propagated in hatcheries beginning about 1900; chum and sockeye salmon were 

propagated beginning about a decade later (Cobb 1930). 

12
The chinook harvest appeared to enjoy a period of relative stability from 1889 to 1920 (Figure 3). 

However, later analysis clearly demonstrated that the apparent stability was an artifact of significant 

qualitative shifts in the fishery (Figure 4). In fact, the prime spring and summer runs were in decline, 

and to maintain the catch, the fishery had shifted to fall chinook (Thompson 1951). After 1920, the 

decline in all races of chinook salmon in the Columbia Basin was obvious. 

Figure 2. Harvest of chinook salmon and the release of chinook salmon 

fry and fingerlings from hatcheries in the Columbia basin (1877-1927). 

(Beiningen 1976; Cobb 1930) 

13
Figure 3. Five year average of chinook harvest in the Columbia River 

(1866-1992). (Beiningen 1976; ODFW & WDF 1993) 

14
Figure 4. Comparison of the seasonal distribution of the chinook harvest in the 

Columbia River in 1878 (A: daily catch per gill net boat) and 1919 (B: weekly catch of 16 

gill net boats and 22 traps). (Source: Thompson 1951) 

In their contemporary analysis of salmon harvests, competent biologists like Willis Rich were 

deceived by the aggregated catch statistics: “the chinook salmon has held up remarkably well...” in

15
spite of an intense fishery, “but the record since 1920 is one of constantly decreasing catches” (Rich 

1948). He attributed the resiliency of chinook salmon and the apparent stable harvest to hatchery 

programs. Rich admitted that he had no evidence that hatcheries were in fact supplementing the 

production of chinook salmon. However, he believed it was “quite possible that there is a causal 

relationship that we do not understand between intensive artificial propagation and the resistance to 

exploitation that the species [chinook salmon] has shown” (Rich 1941). 

Rich’s positive speculation regarding benefits of hatcheries, like Spencer Baird’s earlier 

recommendation, is curious because he had completed the only study of the effectiveness of artificial 

propagation in the Columbia basin. In that study, Rich concluded: 

“... that there is no evidence obtainable from a study of the statistics of the pack and hatchery 

output that artificial propagation has been an effective agent in conserving the supply of 

salmon. The writer wishes to emphasize the fact that the data presented here do not prove 

that artificial propagation may not be an efficient measure in salmon conservation. These 

data prove only that the popular conception, that the maintenance of the pack on the 

Columbia River is due to hatchery operations, is not justified by the available science.”

(Rich 1922). 

During the 1930s and 1940s, questions about the efficacy of artificial propagation, combined with

budget problems during the Depression, resulted in many hatchery closures. Given their poor prior 

performance, hatcheries would not have played a big a role in salmon management in the Columbia

River following World War II except for the fact that rapid construction of mainstem dams required 

a mechanism to address the impact anticipated on fisheries. Artificial propagation was once again 

chosen to compensate for development even though scientific support for that decision was lacking. 

(CBFWA 1990) 

Prior to 1960, hatcheries in the Columbia River contributed little to the overall salmon production 

(CBFWA 1990). After that date, with the development of better disease treatment, more nutritious 

feeds and better hatchery practices, survival from smolt to adult improved dramatically. However, 

the ability to produce large numbers of hatchery adults created a new set of management problems. 

The genetic and ecological effects of hatchery programs are discussed in Section VI of this report. 

16
B. Compensation for Loss of Habitat 

Most of the hatcheries built during this century were intended to mitigate the impact of human 

activities (National Research Council (NRC) 1996). Since the construction of Grand Coulee Dam, 

most of the growth in the hatchery program in the Columbia River has been tied to mitigation for the 

construction of the basin’s hydropower system. Many of the mitigation hatcheries are part of 

specific programs including: 

Grand Coulee Fish Maintenance Project: The first major hatchery program designed to compensate 

for hydroelectric development in the Columbia River Basin was the Grand Coulee Fish Maintenance 

Project. Construction of Grand Coulee Dam blocked access to 1,400 miles of salmon habitat (Fish

and Hanavan, 1948). Salmon production above the dam has been estimated to have been 21,000 to 

25,000 thousand fish (Calkins et al. 1939). This included some of the largest chinook in the 

Columbia River, the so-called "June Hogs." 

With a height of 350 feet from the base of the spillway to the top of the dam, Grand Coulee was too 

high to successfully pass salmon via a ladder or elevator. Salmon managers considered the 

construction of a hatchery immediately below the dam, but engineering problems made an 

alternative necessary. The final plan had three key elements: 1) adult salmon and steelhead were 

trapped in the ladders of Rock Island Dam from 1939 to 1943 and the fish taken to holding areas; 2) 

some adults were released into tributaries below Grand Coulee Dam and allowed to spawn naturally; 

and 3) the remaining fish were held and spawned at Leavenworth hatchery. The streams that 

received the transplanted fish were Wenatchee, Entiat, Methow and Okanogan rivers and Lake 

Osoyoos (Fish and Hanavan 1948). 

The results of the fish maintenance program were evaluated by comparing the contribution of 

relocated stocks to the Columbia River escapement above Bonneville Dam before and after Grand 

Coulee cut off salmon migration. Counts at Rock Island Dam were used as estimates of the 

escapement of relocated stocks. Based on this analysis, Fish and Hanavan (1948) regarded the Grand 

Coulee Salmon Salvage Program a success. However, twenty-four years later Ricker (1972) gave a 

more pessimistic appraisal of the program and concluded that it salvaged nothing. More recently, 

Mullan et al. (1992) concluded that the fish maintenance program conserved the genetic diversity of 

the salmon stocks in the area. An examination of the historical record combined with an analysis of 

allelic variation in the chinook salmon led to the conclusion that the large-scale capture, mixing and 

17
relocation of chinook salmon stocks above Rock Island Dam permanently altered the population 

structure and was the genesis of the present stock structure of salmon in the mid-Columbia (Utter et 

al. 1995). Grand Coulee mitigation is implemented through Entiat, Methow, and Leavenworth 

hatcheries. 

Lower Columbia River Fishery Development Program: The initial Lower Columbia River Fishery 

Development Program (LCRFDP), was strongly influenced by the concepts and design of the Grand 

Coulee Fish Maintenance Project. Originally, LCRFDP had an implementation life of 10 years; 

however, the program has continued to the present with some modifications. The program is closely 

associated with the Mitchell Act, the enabling legislation that permitted federal cost sharing at state 

hatcheries. As the title suggests, the program's initial objective was to concentrate salmon production 

in the lower Columbia River below McNary Dam. At the time, in the late 1940s, it was believed that 

the construction of McNary Dam and the other proposed dams in the upper Columbia and Snake 

rivers eventually would eliminate salmon in the upper basin. In 1956, Congress changed the purpose 

of the LCRFDP by adding fishery restoration above McNary Dam and the word “Lower” was 

dropped from the program title (Delarm et al., 1987). 

The original LCRFDP had six principal parts: 

1. Remove migratory obstructions in the tributaries to the lower Columbia River. This part of the 

program included stream clearance work that removed large woody debris and probably reduced 

habitat quality in some streams; 

2. Clean up pollution in major tributaries like the Willamette River; 

3. Screen water diversions to prevent the loss of juveniles in irrigation ditches, and construct 

fishways over impassable barriers in the tributaries of the lower Columbia River; 

4. Transplant salmon stocks from above McNary Dam to the lower river; 

5. Expand the hatchery program by rebuilding existing hatcheries or new facilities; and 

6. Create salmon refuges by setting aside the lower river tributaries exclusively for the maintenance 

of salmon and steelhead runs (Laythe 1948). 

Stream clearance was consistent with management understandings and attitudes at the time, (e.g., 

WDF 1953), but it is no longer practiced unless the obstruction presents a complete unnatural block 

to migration. The relocation of stocks from the upper to the lower Columbia followed the approach 

18
used in the Grand Coulee program. Artificial propagation was one of six parts of the program, but 

within a few years it became the dominant part (Lichatowich et al. 1996). In 1986, 79 percent of the 

program budget was expended on the hatchery program and about 10 percent on habitat 

improvement and screening of irrigation ditches (the remainder was mainly for administrative costs). 

Today 20 hatcheries are supported through Mitchell Act funds (Table 1). The original goal of the 

LCRFDP was to maintain a harvest of about 32 million pounds of anadromous salmonids from the 

Columbia River (Laythe 1948). However, it was conceded that this might not be possible. 

Table 1. Major hatcheries that are part of the Columbia River fisheries development 

program (Mitchell Act Hatcheries). (Neitzel 1998, personal communication Steve 

Smith NMFS and Rich Berry ODFW)

Facility Name Agency 

First Year 

Operated 

Beaver Creek Hatchery WDFW 1957 

Big Creek Hatchery ODFW 1941 

Bonneville Hatchery ODFW 1909 

Cascade Hatchery ODFW 1959 

Clackamas Hatchery ODFW 1979 

Eagle Creek NFH USFWS 1956 

Elokomin Salmon Hatchery WDFW 1954 

Fallert Creek Hatchery WDFW 1895 

Grays River Salmon Hat. WDFW 1961 

Kalama Hatchery WDFW 1958 

Klaskanine Hatchery ODFW 1911 

Klickitat Salmon Hatchery WDFW 1949 

Little White Salmon NFH USFWS 1989 

North Toutle Salmon Hat. WDFW 1951 

Oxbow Hatchery ODFW 1913 

Ringold Springs Hatchery WDFW 1963 

Sandy Hatchery ODFW 1951 

Skamania Hatchery WDFW 1956 

Spring Creek NFH USFWS 1901 

Washougal Salmon Hat. WDFW 1959 

Mid-Columbia Mitigation: Construction of the five mid-Columbia projects (Priest Rapids, 

Wanapum, Rock Island, Rocky Reach and Wells) eliminated 149 miles of mainstem habitat from

Chief Joseph Dam to the Hanford Reach below Priest Rapids Dam. Spawning and rearing habitat 

was lost from the production of several thousand fall and summer chinook in this reach (NPPC 

1986) with additional impacts to the survival of downstream-migrating salmon produced in 

tributaries above Priest Rapids Dam. 

19
Mitigation programs in the mid-Columbia evolved in three phases. The first phase was the Grand 

Coulee Fish Maintenance Project described above. From 1961 to 1967, four hatcheries and a satellite 

facility were constructed to mitigate for mainstem habitat inundated by the five PUD dams. This 

second phase originally consisted of three spawning channels (Priest Rapids, Turtle Rock and Wells) 

and two conventional hatcheries (Rocky Reach and Chelan). The spawning channels were later 

converted to conventional hatcheries. Implementation of the third phase began in 1989 and is 

composed of the Methow hatchery and two satellite ponds, the Eastbank Hatchery with five 

satellites, and Cassimer Bar Hatchery. This phase is intended to mitigate for juveniles produced in

the tributaries that are lost in passage at Wells and Rock Island dams. 

Lower Snake River Compensation Plan: The Lower Snake River Compensation Plan (LSRCP) was 

developed to mitigate the loss of fish and wildlife resources resulting from the construction of Ice

Harbor, Lower Monumental, Little Goose and Lower Granite dams. Construction of these dams

eliminated 137 miles of mainstem fall and summer chinook habitat and the annual production from 

that reach. The dams also impacted survival of downstream- and upstream-migrating salmon 

produced upstream from Ice Harbor Dam.

The Lower Snake River dams were completed between 1961 and 1975 (Lavier 1976). Planning for 

the program began in 1966, Congress gave its approval in 1976, and the first hatchery (McCall) was 

completed in 1979. Over the next eight years, several other hatcheries and satellite facilities were 

constructed. Currently, there are nine hatcheries funded under the LSRCP (Table 2). The LSRCP 

hatcheries were originally designed as conventional hatcheries, however in some cases, conventional 

hatchery operations have evolved into supplementation programs (e.g., Messmer et al. 1992). 

The Lower Snake River Compensation Program did not include production objectives for Snake 

River coho salmon or Snake River sockeye salmon. Few resources were devoted to Snake River fall 

chinook, with only one hatchery being devoted to this race at Lyons Ferry. Coho salmon populations 

currently are extirpated from the Snake River Basin, sockeye salmon are nearly extinct, and under 

the Endangered Species Act fall chinook are listed as threatened. The adult return goals for the 

Lower Snake River Compensation Program include: 18,300 fall chinook, 58,700 spring/summer 

chinook, and 55,100 summer steelhead (Herrig 1998). 

20
Table 2. Major hatcheries that are part of the Lower Snake River 

Compensation Plan. (Neitzel 1998, Herrig 1998)

Facility Name Agency

First Year 

Operated 

Clearwater Hatchery IDFG 1992 

Hagerman NFH USFWS 1933 

Irrigon Hatchery ODFW 1984 

Lookingglass Hatchery ODFW 1982 

Lyons Ferry Salmon 

Hatchery 

WDFW 1984 

Magic Valley Hatchery IDFG 1987 

McCall Hatchery IDFG 1979 

Sawtooth Hatchery IDFG 1985 

Wallowa Hatchery ODFW 1920 

Other Mitigation Programs: Other mitigation programs include the Willamette River Basin 

hatcheries, and hatcheries operated by Native American tribes and private industry. Five hatcheries 

mitigate for dams constructed in the tributaries of the Willamette River Basin (Table 3). The 

program is funded by the U. S. Army Corps of Engineers. The Nez Perce Tribe has a springwaterfed hatchery developed on Sweetwater Creek near Lewiston, Idaho, and the Yakama Tribe has a 

large state-of-the-art hatchery located near the Yakima River at Cle Elum, Washington. The 

Kootenai Tribe of Idaho has been operating a hatchery near Bonners Ferry, Idaho, originally in 

conjunction with the Idaho Department of Fish and Game, to protect the endangered Kootenai River 

population of white sturgeon from extinction. This facility was just upgraded to more reliably fulfill 

its conservation function, and to address the needs of other at-risk populations in the Kootenai River 

Basin, including native kokanee salmon. Most of the tribal production facilities are funded by 

Bonneville Power Administration ratepayers through the Northwest Power Planning Council's 

Columbia River Basin Fish and Wildlife Program. 

Table 3. Major hatcheries that are part of the Willamette mitigation 

program. (Neitzel 1998)

Facility Name Agency

First Year 

Operated 

Leaburg Hatchery COE 1953 

Marion Forks Hatchery COE 1951 

McKenzie River Hatchery COE 1975 

South Santiam Hatchery ODFW 1968 

Willamette Hatchery COE 1911 

21
Several hatcheries have been financed by private industry to mitigate for loss of salmon and 

steelhead habitat by the construction of dams. Some of the main projects are listed below: 

• The effects of dams constructed in Hells Canyon by the Idaho Power Company are mitigated 

through four hatcheries operated by the Idaho Department of Fish and Game. 

• On the Deschutes River, Round Butte Hatchery mitigates for the construction of Pelton and 

Round Butte Dams by Portland General Electric Company. 

• Two hatcheries on the Cowlitz River mitigate for dams constructed by Tacoma City Light. 

• Two hatcheries on the Lewis River are funded by PacifiCorp to mitigate for hydroelectric 

development on that river. 

As demonstrated by the history of artificial production in the Columbia River system, there has been 

extensive variation in how hatcheries have been used to address needs of fisheries management. In 

the earlier years, the basis on which hatcheries were developed was opinion and adherence to a 

popular concept for increasing the magnitude of salmon runs. As hatchery programs developed 

better technology over the years, there were concomitant changes in what constituted hatchery 

management policy, and changes in the extent to which biological rationale influenced that policy. 

There have been differences in the quality of hatchery fish and improvements in the survival 

performance of fish released from hatcheries, but also a performance that has been highly variable 

among hatcheries. It is instructive, therefore, to look simultaneously at the evolution of the role of 

science as the hatchery concept developed and at the history of hatcheries on the Columbia. 

22
Figure 5. Columbia River Basin state, tribal and federal hatchery locations. 

IV. Scientific Foundation

All salmon management programs are derived from a scientific foundation -- a set of assumptions, 

theories and principles that describe how the salmon ecosystem functions (ISG 1996 The foundation 

is a powerful part of any management program. It is used to interpret information, identify problems 

(impediments to achieving objectives) and select restoration strategies. Unfortunately the conceptual 

foundation is rarely explicitly stated or evaluated, and as a consequence programs can suffer from

errors in concept. When limited scientific inquiry and false assumptions are a part of the process, 

the program derived from them will have a high likelihood of failure. 

The conceptual foundation of the Columbia River hatchery program has never been specified or 

examined in detail. In this section, we describe the set of assumptions we believe were the basis of 

the hatchery program. Because it has never been explicitly stated, the conceptual foundation 

described here had to be derived from our review of the program -- its apparent objectives, 

assumptions stated by practitioners and its measures of performance. The conceptual foundation we

present is thus qualified as our interpretation of the historical record, and accounts for the period 

23
ending in the 1960s; the point at which the hatchery assessment (the second phase of our report) 

begins. 

A. The Early Conceptual Foundation of Hatcheries 

The early hatchery program was consistent with the overarching assumption that salmonid 

production systems could be simplified, controlled, and made more productive. Hatchery 

technology not only simplified and controlled production, it circumvented the need for natural 

ecological processes and freshwater habitat. This philosophy was also reflected in the subsequent 

development of resident fish hatcheries. The program intention was simply to increase catch by 

protecting the eggs, maximizing the number of fry released, and harvest fish returning from the sea. 

Given the hypothetical fecundity of 3,000 eggs, a spawning pair may successfully produce 

something in the neighborhood of 500 fry to emergence under natural stream conditions. Under the 

same scenario, artificially spawning and incubating those 3,000 eggs would result in about 2,500 fry 

to emergence under the hatchery scenario, or a five-fold increase over natural incubation because of 

the protection against predation, disease, poor incubation conditions and scouring floods. So the 

rationale of the early practitioners was not an unreasonable expectation of the advantage of hatchery 

fry production. Moreover, it was a technique that, when properly employed, had brought 

substantive results, as demonstrated by an example we discuss in the next section (B). 

The problem in the beginning was one of dimension. Even with a five-fold improvement in egg 

survival, the number of females intercepted was insignificant compared to the number spawning 

naturally, even when the run was seriously depressed. The primary problem, however, was that fry 

were distributed to a variety of streams with little or no information about the suitability of habitat or 

risk for young fish. This also was true of the often haphazard stocking of non-native or exotic fish. 

In Idaho alone, 30 exotic species of resident fish have been introduced since the late 1890s. 

(Simpson and Wallace, 1982). 

It was the natural extension of the concept that if protecting the incubating eggs from such harm

would result in a five-fold improvement in fry production, and hence the extrapolation to a five-fold 

improvement in adult returns, then why not control the rest of freshwater rearing to reduce losses 

from predation, disease, starvation, and environmental alterations in the natural stream? Therefore, 

taking the simple equation one step farther, of the 500 wild fry emerging naturally, 45 might be 

24
expected to reach the smolt stage and enter marine waters, from which two to five adults would 

return. However, extrapolating the hatchery survival advantage to the next life history stage, if the 

now 2,500 fry successfully incubated from 3,000 eggs in the hatchery were reared and protected 

through the succeeding freshwater rearing period, 2,000 fingerlings could be produced to the smolt 

stage, equating to a total hatchery production benefit nearly 44 times greater than natural production 

of the original 3,000 eggs. Rather than two to five adults returning per pair of natural spawners, 

given marine survival equal to natural fry, the hatchery benefit would equate to over 100 returning 

adults from the same pair of spawners. The simple extrapolation of hatchery survival to return 

success was the presumptive expectation of the hatchery enthusiasts, and the basis for the expansion 

of the hatchery building program that has spanned a half century to the present distribution of 

artificial production throughout the Columbia basin (Figure 5). 

Experience has demonstrated, however, that successful production of juveniles in hatcheries is not so 

simple and that hatchery production by itself cannot guarantee a sustained increase in catch. 

However, the point in laboring the expectation that ushered in the development of hatcheries is that 

the fundamental premise is very similar to the basic assumption inherent in the subsequent 

development of Pacific salmon and many resident fish hatcheries throughout the Pacific Northwest. 

That presumptive view has not changed substantially, and production augmentation currently is 

being undertaken in at least the Columbia River Fishery Development Program, but with a more 

conservative expectation of benefit. 

Part of the problem is that early salmon managers viewed rivers as agri-ecosystems capable of being 

simplified, controlled and through cultivation (artificial propagation) brought to higher levels of 

production (Bottom 1997; Lichatowich et al. 1996). The agricultural approach to management led to 

an emphasis on single species production objectives that separated the development of fisheries 

science from the major developments in ecology for anadromous and resident species. Fisheries 

adopted agricultural objectives and supporting science instead of the holistic approach advocated by 

early fisheries workers such as Forbes (McIntosh 1985; Bottom 1997). Viewing rivers as farms led 

to the belief that individual enterprise alone could overcome any natural limits to production 

(OSBFC 1890). As late as 1960, the Washington Department of Fisheries still believed that fish 

farming was closely linked to farming on land and shared the same principles and rewards (WDF 

1960). 

25
An agricultural model for salmon production was expressed by several early salmon managers. The 

following is a sample of their statements: 

“Professor Baird often said ‘one acre of water was worth seven acres of land, if properly 

cultivated, ‘ but I am convinced that the Professor erred only in this, that I believe one acre 

of the waters of any salmon stream in Oregon, if judiciously cultivated under favorable 

circumstances, and if not paralyzed by ignorant vicious legislation, is worth more as a 

medium for the product of a food supply than forty acres of the best land in the State.”

(Hume, 1893) 

“It has been the habit to cultivate the land and neglect the water.... We have tilled the 

ground four thousand years; we have just begun to till the water.... Less care and labor are 

needed to raise fish than to raise other animals, or even to raise vegetables.” (Oregon State 

Board of Fish Commissioners, 1890) 

“Modern incubation equipment for fish propagation compares with greenhouse methods to 

increase the survival of plants... As man makes ready the soil for growing of better crops, so 

may he improve the water for the growing of fish. The steps to be taken in the harvest of 

surplus seed, the surplus crops, the preparation of land or water follows the same 

fundamental requirements.” (Washington Department of Fisheries 1960) 

Commercial aquaculture, or fish husbandry for commercial markets with other agricultural 

commodities in the Pacific Northwest, has demonstrated production capabilities even better than the 

original hatchery practitioners envisioned. This is because fish farmers control the entire life cycle 

from spawning to adult harvest and realize the equivalent of 1,800 marketable adult-size fish per 

spawning pair. However, while the application of agricultural principles has been beneficial in some 

aquacultural enterprises, it generally has failed when applied to anadromous salmonids, which are 

released to experience more than three-quarters of their life in the natural environment. 

In retrospect, when we look back to the era of “farming nature," in light of the major leaps that 

agriculture has made and continues to make in animal husbandry, the assumption that watersheds 

could be treated as farms and managed like agricultural enterprises was understandable. This logic 

led to the belief that natural limits on production could be ignored and, through fish culture levels of

26
production greatly increased. Initially production from natural populations was assumed to be 

limited by spawning success, and production of the ocean relatively unlimited. Consequently, it was 

believed that increased survival of fry and fingerlings in the hatchery would translate 

proportionately to increased adult return. This is epitomized in the following excerpts.

"It is imperative, therefore, that some means be adopted to counteract the depletions arising 

from this source (habitat degradation); but the most important reason for the artificial 

propagation is the fact that the natural method is extremely wasteful, which is not true of the 

artificial method." (Smith 1919, p. 6) 

"In my opinion, if the salmon runs of this state are to be maintained and increased, it is going 

to be necessary to constantly construct new hatcheries. The much greater effectiveness of 

hatchery operations, as compared with natural propagation, has in my judgment been so 

effectively proven as to no longer permit discussions among those who are acquainted with 

the situation." (WDFG 1921, p. 17) 

"There can be no doubt in the mind of anyone who has studied the question, that the future 

prosperity of our salmon fisheries depend largely upon artificial propagation... I am

convinced that not more than 10 percent of the ova spawned in the open streams are hatched, 

owing principally to spawn-eating fish that prey on them... while from artificial propagation 

90 percent are successfully hatched. What more need be said in favor of fish culture?"

(Oregon State Fish and Game Protector 1896, p. 33) 

“Nature ... produces great quantities of seed that nature does not utilize or need. It looks 

like a vast store that has been provided for nature, to hold in reserve against the time when 

the increased population of the earth should need it and the sagacity of man should utilize it. 

At all events nature has never utilized this reserve, and man finds it already here to meet his 

wants.” (Stone 1884, p. 21) 

The assumptions that watersheds could be made more productive through agricultural practices and 

that natural limits on production could be circumvented were the foundation of the Columbia Basin 

hatchery program. Moreover, hatchery production was assumed to be additive to natural production, 

with no interaction or impact on natural populations. Given the expected translation of hatchery 

27
survival to adult returns, practitioners also assumed that the principle measure of success for a 

production hatchery should be the numbers of juveniles released. Obviously, there would be an 

associated expectation that harvest level should also increase, but accounting for catch over many 

fisheries and jurisdictions was much more difficult and less practical than simply monitoring 

numbers of juveniles produced. 

In summary, the fundamental assumptions governing the development of the Columbia River 

hatchery program before 1960, and the genesis of the early conceptual foundation of hatchery 

production, was centered on five general assertions: 

• It was not only possible but also desirable to simplify and control production of anadromous 

salmonids to increase their abundance. 

• Anadromous salmonids could be effectively managed through the application of agricultural 

practices and science. 

• Production limitations during freshwater life stages could be circumvented by hatcheries, and the 

capacity of the ocean was relatively unlimited. 

• Artificially propagated fish released to the rivers added to production from natural populations. 

There were no negative interactions. 

• The probability of success was so high that evaluation of adult returns was not necessary.

B. The hatchery framework as an adaptive process 

Development of a conceptual foundation applicable to Columbia basin hatchery programs has to be 

consistent with what is known about salmonid life history and ecological processes. Any fisheries 

management effort that does not integrate the management criteria around the inherent life history 

strategies that have evolved among the specific salmonid and native resident fish species, including 

stock-specific differences, will fail. Pacific salmonids have evolved specific life history patterns and 

population structures compatible with their native habitat (Brannon, in press), and ignorance, or 

disregard, of that compatibility will weigh heavily against any management attempts to sustain or 

build wild fish populations. In essence, the conceptual foundation must be flexible enough to 

accommodate derivations in life histories among all fish species, including those differences within 

the mixture of stocks representing the species. 

28
Natural populations of salmonids are genetically programmed to survive and behave in ways that 

maximize long-term fitness in their natural environments. Disconnecting the organismic and 

environmental linkages effectively disrupts the timing and reduces fitness back to the level of a 

founding population. Survival success returns to the odds of happenstance, and adaptive evolution 

must start over again. Typical central hatchery programs that follow such management plans, and 

repeatedly distribute fish around the watershed can not effectively address the concept of ecosystem 

management. These fish will have little contribution value to natural production, and by continually 

or even intermittently spreading stocks around the system, fish will remain biologically incompetent 

for those foreign environments. 

The challenge in developing the conceptual foundation for hatcheries is to re-prioritize production 

and operation goals to address the biological needs of the stock being propagated. In freshwater, 

chinook life history strategy is the most complex among the anadromous salmonids and pink salmon 

the simplest, with coho, steelhead, sockeye, and chum salmon intermediate. Stream-dwelling 

species, such as chinook, coho and steelhead, are limited most often by the rearing capacity of their 

stream. Generally, factors associated with spatial and nutritional requirements of stream-dwelling 

salmonids determine the upper limit of population biomass that can be sustained within the stream, 

and strategies to maximize productivity around those parameters evolve to define the population. 

Sockeye, chum, and pink salmon use freshwater streams only for spawning, with the juveniles 

immediately migrating to their nursery environments in lake (sockeye) or marine (chum and pink) 

waters for rearing. Only the spawning area of the stream generally limits these species, as the 

productivity of their nursery environment most often exceeds the capacity of the spawning grounds 

available. 

In developing a conceptual foundation for hatchery programs, the process must allow for 

differences inherent in the fish targeted and whether they have adopted anadromous or resident life 

histories. It appears that successful applications of the hatchery concept are those cases that do not 

deviate significantly from the biological repertoire of the fish, and were successful in addressing the 

limiting factors in the natural life history of the species. The Prince William Sound (PWS) pink 

salmon hatchery program is a good example (Linley, in press). In the early 1970s the commercial 

fishery on pink salmon was threatened by the low return of fish into the sound, and hence it was 

believed the relatively small numbers of fry naturally produced were insufficient to rebuild the run. 

29
The non-profit hatchery program was started, involving the artificial spawning and incubation of fry 

for release into PWS. Fry releases were synchronized with the beginning of the spring plankton 

bloom, which was the biological optimum for rapid growth. Their success was unprecedented 

(Figure 6). Adult returns improved four-fold over the previous ten-year average of 5 million adults, 

and has reached numbers as high as 45 million returning fish. Percent survival of fry released to 

achieve those levels of return success ranged from 0.9 percent to 13.0 percent (Figure 7) at the 

Armin F. Koernig hatchery (Linley, in press), far exceeding the survival performance of any 

fingerling or smolt production hatchery on the Columbia. The survival variability was attributed to 

variations in marine productivity, temperatures, and predation, based on annual monitoring of those 

conditions in the sound (Willette 1992). Success in the PWS hatchery program was experienced by 

working within the life history definition of the species, and has succeeded for ten generations. 

Similar success addressing production restraints from loss of habitat was experienced with sockeye 

returning to Weaver Creek on the Fraser River (IPSFC and PSC annual reports). Logging had 

caused high variability in flows, and the loss of redds and low returns were threatening the viability 

of the run. The Salmon Commission built an artificial spawning channel on the stream in which 

flow was controlled and much of the silt and fine material prevented from infiltrating the graded 

spawning substrate. Natural spawners used the channel with egg-to-fry survival rates averaging well 

over 60 percent, or about 10-fold better than survival in the adjacent stream. Adult returns showed a 

marked improvement, amounting to an average of about 250,000 fish annually (Figure 8). 

30
Figure 6. Annual run size of pink salmon returning to hatchery and 

natural production streams in Prince William Sound, Alaska.

Figure 7. Percent survival of pink salmon fry released from

Armin F. Koernig hatchery in Prince William Sound, Alaska.

31
Figure 8. Annual run size of sockeye salmon returning to 

Weaver Creek in British Columbia (IPSFC/PSC Rept). 

The Weaver Creek channel (hatchery) concept succeeded because the operation was complementary 

to the biology of the species, and addressed only that portion of the life history that was limiting the 

population. In both the PWS pink salmon hatchery program and the Weaver Creek sockeye salmon 

spawning channel, the conceptual foundation was consistent with the species life history and 

integrated the solution to the production problem effectively. However, these species present a 

different kind of challenge than that facing the Columbia basin hatcheries. Sockeye and pink salmon 

are normally limited by freshwater spawning area, and the hatchery approaches used in both cases 

addressed that limitation with relatively minimal intrusion in the ecological system. The streamdwelling species (chinook, coho, and steelhead) create a different problem when limited rearing 

habitat is the primary source of population decline. Hatchery rearing programs have a more difficult 

task of integrating cultured fish into the natural system because, unlike artificial incubation 

programs, under present hatchery rearing environments the fish are removed from everything that 

would resemble or prepare them for the natural stream environment they must compete in once they 

are released. However, even under these conditions, hatchery programs have shown success in 

increasing production. The Makah Nation Fish Hatchery is a good example. 

32
In the late 1970s, the Makah Indian Nation sought to increase the production of anadromous 

salmonids associated with the streams on their reservation in far northwestern Washington state. The 

Sooes River chinook population was being seriously threatened by clear-cut logging watershed 

instability, runoff from log yards, and overfishing by the coastal and Canadian fisheries. Fewer than 

100 fish were reaching the spawning grounds in some years. In cooperation with the USFWS, the 

Makah National Fish Hatchery was built on the Sooes River, entering the Pacific Ocean just south of

Cape Flattery. Plans were initiated to introduce chinook from other hatcheries, but the Makahs 

insisted that only Sooes chinook be propagated, even if the hatchery was not fully utilized in the first 

few years. They felt Sooes River fall chinook were uniquely adapted to that coastal system, with 

large eggs and an early migration timing to marine waters. Therefore, the hatchery program was to 

enhance the Sooes River chinook population, and a breeding plan was followed to maintain the 

diversity present. Fish excess to hatchery needs were permitted to spawn naturally, and in theory 

both the hatchery population and the naturally spawning fish commingled as a single population. 

Age-3 returns from hatchery propagation started in 1984, and by 1988 hatchery contributions were a 

significant share of the total return (Figure 9). By the late 1990s well over 2,000 fish were returning 

from both the hatchery and the natural production. 

Figure 9. Chinook salmon annual return to Sooes River, 

 Washington, from hatchery and natural production. 

33
The Sooes River chinook salmon hatchery program success is attributed in part to the emphasis on 

the native stock. The selective advantage of the adaptive traits manifest in the physical and 

behavioral characteristics of the Sooes stock were not compromised by introductions of another 

stock that would have been incompatible with that coastal system. Also contributing to their success

is the hatchery's proximity to the marine environment. Naturally produced fish have a relatively 

brief period of freshwater residence, and the hatchery fish can be in brackish water within an hour 

after release from the hatchery. 

These examples of pink, sockeye, and chinook hatchery programs that have had good success in 

reaching their production objectives demonstrate that the appropriate conceptual framework is 

critically important to the development of functional enhancement systems. Admittedly, none of the 

above examples is subject to the severely anomalous conditions facing Columbia River salmon and 

steelhead. The point in fact, however, is that if Columbia Basin hatcheries are to have success in 

enhancing natural production and restoring some of the runs to self-sustaining populations, the 

conceptual foundation has to be that much more specific to the task. To meet the challenge of 

integrating artificial propagation into the Columbia Basin ecosystem and reach the commercial, 

tribal, and public fishery objectives, the model has to be rigorously defined and the biology of the 

component species well understood. 

Many of the previous requirements for successful anadromous salmonid hatchery programs also 

apply directly to resident fish. As with the previous examples of successes with pink, sockeye, and 

chinook salmon, resident fish hatcheries also share the success of meeting their goals. It is important 

to note that the goals of anadromous and resident fish hatchery programs can differ considerably due 

to differences in program application and purpose, as well as differences in life history strategies 

and requirements of the species targeted. Nonetheless, the two following examples of successful 

resident fish hatchery programs provide substantial recreational fishing opportunities, increased 

numbers of angler trips, and very important local economic benefits. Their success was judged by 

the contribution of recreational fisheries to the local economies and the quality of life in the interior 

Columbia Basin. These two examples involve Sprague Lake in eastern Washington, and Lake 

Roosevelt, in northeastern Washington. 

Resident hatchery stocks of rainbow trout and Lahontan cutthroat trout were successfully 

introduced into Sprague Lake following complete elimination of carp , stunted yellow perch and 

34
additional undesirable non-native fish species through the use of rotenone (Whalen 1989; Willms

1989; Willms et al. 1989). Prior to rotenone treatment, and the introduction of rainbow and cutthroat 

trout, the estimated annual angler pressure was believed to be approximately 1,700 angler days 

(approximately 13,600 angler-hours; Willms et al. 1989). Following rotenone treatment, removal of 

undesirable species, and introduction of rainbow and cutthroat trout, the estimated 13,600 anglerhours rose to over 200,000 in 1987 and 1988 (Figure 10; Willms et al. 1989). One of the goals of 

this resident trout introduction program was to generate $500,000 annually for the local economy. 

The program has since provided over $1 million annually to the local economy - 20 times the 

original target goal (Willms et al. 1989). These authors also determined that in 1986, 46.6 percent 

of all rainbow trout stocked into Sprague Lake were returned to the creel during the same year. This 

return is more than forty times that of documented adult anadromous salmon returns, which 

illustrates the need for separate and appropriate evaluation criteria of resident and anadromous fish 

hatchery programs. In this case, the newly established resident trout fishery in Sprague Lake 

illustrates the benefits of resident hatchery programs, which provided a popular fishery in a 

previously little-used lake. 

The second example of successful resident fish hatchery programs involves Lake Roosevelt, the 

Spokane Indian Tribe's resident fish hatchery, and rainbow trout. The Spokane Tribal Hatchery 

program began stocking Lake Roosevelt with rainbow trout and kokanee salmon in 1991 in order to 

establish and enhance resident fisheries in the lake as mitigation for anadromous salmon resources

permanently lost due to dam construction. From 1991 through 1994, rainbow trout catches 

increased nearly five-fold (Figure 11 ), angler trips nearly tripled ((Figure 12), and estimated annual 

revenue generated by hatchery-supported resident fisheries increased nearly four-fold (Figure 13, 

Cichosz et al. 1996). 

35
Figure 10. Comparison of angler-hours during pre-stocking

(1985) and post-stocking (1987, 1988) periods at Sprague

Lake, Washington (Data from Willms et al. 1989)

0

50,000

100,000

150,000

200,000

250,000

Years

1985 1986 1987 1988

Figure 11. Comparison of rainbow trout catch before (1990,1991)

after stocking (1992-1994) in Lake Roosevelt (Data from Cichosz et

1996).

0

100,000

200,000

300,000

400,000

500,000

600,000

1990 1991 1992 1993 1994

Year

36
Figure 12. Comparison of angler-trips on Lake Roosevelt before

and after rainbow trout stocking (Data from Cichosz et al.)

0

100,000

200,000

300,000

400,000

500,000

600,000

700,000

1990 1991 1992 1993 1994

Year

Figure 13. Comparison of economic value (millions of dollars) of

fishery before (1990) and after rainbow trout stocking program (Data

Cichoz et al.1996)

0

5

10

15

20

25

1990 1991 1992 1993 1994

Year

V. Organization and Classification of Artificial Production

We have stated that implicit in the artificial production of salmon, and the fundamental premise 

behind development of salmon hatcheries in the basin, was the belief that increases in the number of 

juvenile salmon produced and released from hatcheries would result in a proportional increase of 

harvestable adults. Although expectations of artificial production have matured to something more 

37
qualified by experience, that basic premise has continued to be a strong impetus behind hatchery 

substitution for habitat loss and reduced access to historical spawning grounds. New hatcheries are 

being constructed in anticipation of markedly increased adult returns resulting from such operations. 

How these new hatchery complexes integrate into the basin ecosystem will be defined by how 

management applies the conceptual framework to meet the objectives they have for the fishery. 

The application of the hatchery model in the management of salmon fisheries, and hence the basis on 

which performance of such hatcheries must be judged, depends entirely on the objectives or 

strategies being addressed (Table 5). With the possible exception of hatcheries that are used solely 

to restore specific populations nearing extirpation, all anadromous and resident fish hatcheries are 

intended to provide fish for harvest. Management strategies fall under two categories of purpose, 

one to augment natural production for harvest, and the other to mitigate for the loss of harvest as a 

result of the diminution or elimination of salmon-producing habitat, and excluding their access to 

that habitat. It is instructive, therefore, to define more precisely the nature of augmentation and 

mitigation in the Columbia basin because of their application in mandates of Congress to enhance 

production or compensate for its loss as the river has developed around other societal needs. It is 

also essential to understand the classification of hatcheries in this document if assessment of past 

performance and current status is to provide the intended framework on which future management

decisions and policies will be based. 

A. Harvest Augmentation 

Early in the development of mid-nineteenth century salmon fisheries, and as commercial harvests of 

Columbia River chinook salmon were doubling every season, artificial production was given serious 

consideration as a means to augment the harvest of salmon beyond that which could be sustained by 

natural production. Freshwater production of young salmon in natural river systems was correctly 

assumed to be limited by spawning success and habitat, and hatcheries were conceived as a means to 

overcome such constraints on natural production. The fact that egg-to-fry survival could be 

increased as much as ten-fold through the process of artificial spawning and incubation in hatcheries 

was the general motivation behind construction of the first Columbia Basin hatchery in 1876, located 

on the Clackamas River. The expectation followed that adult returns would materialize from such 

technological interventions, reminiscent of philosophical deductions from technological 

advancements in agriculture and animal husbandry. This same pervasive philosophy was 

incorporated into the development and maintenance of mitigation hatcheries that propagated resident 

38
fish species. Overfishing reduced the abundance of anadromous salmonids so extensively in the 

basin that augmentation actually tried to compensate for the fishery and was never able to expand 

harvests beyond historical natural production. 

Although attempts to assess hatchery contribution to the harvest did not occur until more recent 

times, and in spite of divided opinion within the scientific community about hatchery success (Lythe, 

1948), the belief that artificial production contributed to the fishery has been responsible for 

development of substantial hatchery effort. There were three fundamental assumptions associated 

with the use of hatcheries for the purpose of harvest augmentation. (1) the freshwater environment 

limits natural production, (2) ocean carrying capacity exceeds natural production potential, and (3) 

hatchery production will not negatively impact natural populations. Belief in these assumptions still 

prevails, and they exist as criteria that need to be carefully assessed in applications of harvest 

augmentation programs to justify use of such technology for that objective in the Columbia River. 

The first and second assumptions have credence, but the lower end of the productivity threshold in 

the marine environment is a very powerful limiting force on production, regardless of the magnitude 

of production in freshwater. Augmentation of harvest through hatchery production has been 

demonstrated most recently with pink salmon in Prince William Sound as seen in Figure 6, and 

highly correlated with marine conditions (Willette, 1992). Several hatchery programs in Alaska 

demonstrate very positive augmentation success, routinely above 10-percent survival of fingerling

sockeye, and higher than 20 percent among some groups on fingerling coho (Marianne McNair, 

ADF&G, personal communication). 

Successful augmentation hatchery programs are not rare in Washington and Oregon, either. The old 

Washington Department of Fisheries was formed to manage marine fisheries in the state specifically 

for commercial harvest, and augmentation was the objective of Washington State hatcheries. Hood 

Canal chum salmon hatchery production is a good example (Fuss, 1998). The size of the chum

salmon run in Hood Canal has been directly related to the level of hatchery fry releases (Figure 14). 

39
Figure 14. A comparison of Hood Canal chum salmon 

 releases and subsequent run size. (Fuss 1989) 

Similarly, coho production in Puget Sound shows a strong relationship between hatchery production 

and return run size. Fuss (1998) points out however, that regardless of hatchery contributions, if the 

environmental restraints are limiting the carrying capacity, production levels off or declines to 

whatever the environment will support (Figure 15). 

Figure 15. A comparison of hatchery releases of Puget 

Sound 1+ coho with subsequent run size. (Fuss 1998) 

40
In the context of ecosystem management, the second and third assumptions listed above create major 

problems for attempts to accommodate harvest augmentation objectives. Ecosystem management

and harvest augmentation are basically conflicting strategies that must be resolved consistent with 

the long-range goals for the fishery. The real question is not whether hatcheries are able to 

successfully produce salmon and steelhead artificially; that has been demonstrated many times. The 

deciding issue is whether hatchery production can integrate within the ecological framework on 

which future salmon management is proposed to operate. It follows, therefore, that before resolution 

can be addressed on the use of augmentation strategy in the Columbia River, careful assessment of 

harvest augmentation success through the use of hatcheries outside the basin, and the measured 

ecological impacts, should be undertaken. 

B. Mitigation 

With the development of water resources in the Columbia River, about 40 percent of the originally 

accessible river system is now inaccessible to salmon, and much of the remaining habitat has been

significantly compromised for incubation and rearing. These losses were mitigated through artificial 

propagation, and major hatchery programs now prevail in the Columbia River system, and currently 

represent a significant and continuing investment. Conceptually, mitigation hatcheries are meant to

replace harvest potentially lost as a result of habitat alteration. These losses, related to dams, water 

diversions, and habitat degradation, have been justified or made "socially acceptable" (Christie et al., 

1987) by the precept that the resulting losses in natural production of salmon would be compensated 

through hatchery production of anadromous and resident species. Consequently, with the extensive 

development of the Columbia River, most of the 93 artificial production facilities (hatcheries, ponds, 

and release sites) in the river system are operated for mitigation purposes. 

There is concern that these major program developments, like augmentation, have progressed 

extensively without careful assessment of their effectiveness in meeting their primary objectives. 

The problem in making such assessments of mitigation hatcheries on the Columbia, however, is that 

their application has been somewhat equivocal, with some taking on a distinct augmentation role to 

increase harvest, while others have been applied in supplementation to strengthen the numerical base 

of wild populations. With the decline of naturally reproducing stocks of salmon and resident fish 

throughout the Columbia River Basin, and the contemplated further use of hatcheries to overcome 

these losses, assessment of their effectiveness, limitations, and application must be made. Mitigation 

41
must also be viewed in the broader perspective of its present use in the Basin, including measures to 

stem the risk of extinction. Classification of mitigation hatcheries, therefore, fall within four 

different categories associated with degrees of salmon extirpation, including maintenance, recovery, 

preservation, and restoration. An additional category of resident fish hatcheries involves resident 

fish substitution programs, such as those discussed on pages 34 and 35 of this report and in the 

Northwest Power Planning Council's Columbia River Basin Fish and Wildlife Program. These 

hatcheries propagate resident fish for harvest as either on-site or off-site mitigation for lost salmon 

resources. Here is a more detailed look at the four classifications of mitigation hatcheries: 

(1) Maintenance 

Maintenance is consistent with the original objective of mitigation as a mechanism to maintain those 

runs of salmon that would otherwise be reduced or extirpated by river developments resulting from 

habitat degradation or migratory impasse. For example, with the construction of dams on the river, 

especially those without fish passage, the risk of partial or total loss of the run was mitigated by 

replacement with hatchery fish. The objective is maintenance of the pre-existing run of salmon at or 

near its previous abundance. Maintenance hatcheries may substitute or circumvent the need for 

natural habitat, characterized by attempts to mitigate development of the hydro-system in the upper 

Columbia and Snake rivers, or they can supplement the number of naturally spawning salmon 

affected by development. Maintenance, in its most basic rendition, is to maintain contribution of 

salmon and steelhead approximate to those levels immediately preceding developments affecting 

their productivity. 

With the present emphasis on sustaining natural runs of salmon, supplementation has taken a much 

greater role in maintenance conservation. Conceptually, supplementation is meant to reinforce 

populations without loss of the genetic structure. Supplementation, therefore, is employed to 

enhance the native stocks of salmon and steelhead by increasing their reproductive base through 

artificial propagation, using only the native gene pool in the process. 

(2) Recovery 

Recovery has become an increasing responsibility of mitigation. Compelled by the decline of salmon 

and steelhead in the Columbia system, major efforts are being expended on rebuilding runs to levels 

that are considered sustaining under the stress imposed on these populations in the migratory 

corridor of the mainstem river, and the condition of their endemic habitat. In the context of 

42
mitigation with emphasis on native populations, supplementation is by definition the rebuilding of 

the native population of anadromous salmonids. Application of artificial propagation in rebuilding 

populations has been thwarted by the disregard of population genetics and careful breeding programs

(Remain and Ståhl, 1980; Allendorf and Utter, 1979; Cross and King, 1983), as well as poor 

conditioning of fish while in the hatchery environment (Swain and Riddell, 1990). Salmonids have 

evolved to be compatible with their environments, and each population, therefore, has adapted to the 

specific characteristics of their respective habitat. Spawning time, emergence timing, juvenile 

distribution, marine orientation and distribution are not random, but occur in specific patterns of time

and space for each population (Brannon, 1984). In the technical sense, therefore, enhancement of 

specific wild salmonids must observe this compatibility between native stocks and their 

environments., This perspective is a central theme of mitigation for recovery for all native 

anadromous and resident fish species in the basin. 

(3) Preservation 

Preservation is the most extreme measure used to prevent extinction, and characteristically has been 

implemented when numbers have degenerated to such low levels that risks associated with 

emigration and marine life phases threaten extinction. Preservation is approached along two 

different avenues. The first is to increase the numerical base in captivity through maintenance of 

captive brood stock. Maximizing reproductive potential under captive breeding over two 

generations can provide the numerical advantage and genetic predisposition necessary for recovery. 

Such a preservation approach is meant to be short-term, involving only a limited number of 

generations. However, when a major cause of the decline persists, such as the problems with the 

migratory corridor on the Snake and Columbia rivers or habitat destruction or overfishing, for 

example, then such preservation programs may have to continue until conditions favor natural 

recovery. 

The second avenue in preservation is to provide repositories of genetic diversity for future 

introduction and recovery. Captive brood can be applied in such approaches, but germ plasm

repositories are the most feasible, inexpensive, long-term approach. Rather than the "choice of last

resort," germ plasm preservation should be proactively included in routine population recovery 

measures. Healthy populations need to be the target for gamete cryopreservation to assure that 

repositories contain representative genetic diversity, and from which domestication and inbreeding 

can be avoided in mitigation hatcheries. Both avenues are meant to preserve genetic diversity or to 

43
keep stocks from demographic extinction, and assist in recovery when habitat and migratory passage 

are restored.

(4) Restoration 

Restoration is the re-establishment of a salmon or steelhead run in the place of an extirpated natural 

population. Understandably, establishing a successfully reproducing run requires sufficient 

similarity between the introduced fish and the extirpated population to ensure compatibility with 

controlling environmental phenomena. Matching genetic predispositions to optimize the likelihood 

of success is key to the restoration strategy. Important among the environmental factors are winter 

stream temperatures and length of the freshwater migratory pathway. These features determine 

timing and distribution patterns of native stocks. The optimum strategy is to use these features to 

select candidates for introduction most like those demonstrated by the native phenotype. 

Restoration mitigation is a difficult task, and necessarily of greater duration to realize functional reestablishment of a run because of the generation time required for the adaptive evolution or recreation of the appropriate form. The critical measure of success is not the number of returning fish 

to the hatchery. Hatchery environments are secure and forgiving of timing inconsistencies that can

easily be amended by feeding programs that exaggerate size at time of release. Restoration criteria 

must target only the naturally reproducing segment of the run, and hatchery programming should be 

altered to accommodate the spawning, incubation and migratory timing patterns evolving among 

those fish. Differentiation between what is observed among hatchery contributions and returns from

natural reproduction is a difficult and long-term process, but restoration cannot be accomplished 

with anything less. To have successful restoration is to have established a self-perpetuating wild 

run, free of hatchery dependence. 

C. Determinants of Performance 

In determining the performance of anadromous salmonid augmentation and mitigation hatcheries, it 

is apparent that the objective identifies the determinant criteria. Moreover, the criteria are only 

satisfied in terms of the adult return response, as measured in the harvest fishery or the return 

destination. Augmentation has the objective of increased harvest, or contribution of returning adults 

to the fishery. Mitigation has the objectives associated with maintenance, recovery, preservation, or 

restoration measured as contribution of reproductive adults in the target population. In both 

augmentation and mitigation hatchery programs, genetic and demographic concerns must be 

44
addressed. In the former, if genetic compatibility is not a management concern, then isolation of the 

returning fish from neighboring native stocks must be at least be assured or the level of straying nonconsequential. In the latter, genetic identity and diversity are basic to the objectives sought in each 

of the mitigation functions. In this particular document, the key assessment criteria are listed below, 

and apply to both augmentation and mitigation programs. 

1) Has the hatchery achieved its objective? 

2) Has the hatchery incurred costs to natural production? 

3) Are there genetic impacts associated with the hatchery production?

4) Is the benefit greater than the cost? 

These criteria are relatively simple and straightforward. However, their resolution has an uncertain

complexity because of the overriding influence of marine conditions, the effects of mixed stock 

fisheries, interaction among runs of fish, and the influences of the dynamic interaction within 

ecological communities on the ultimate return success of a run. Therefore, in as much as it is 

possible, the performance measures involved in the SRT assessment will be qualified based on 

relative information on annual variations in marine productivity, temperature trends and associated 

predator occurrence, distance up the freshwater migratory corridor, and other controlling influences 

unrelated to the actual hatchery variables involved. 

Artificial production of resident fish in the Columbia Basin should not be evaluated using specific 

Basin anadromous salmonid propagation criteria for several reasons. First, the purposes of 

anadromous and resident fish propagation programs may be considerably different. For example, a 

resident fish artificial propagation program may represent mitigation for an extinct salmon run, 

extirpated by blockage of its spawning habitat by dams. Mitigation using resident fish programs or 

exotic fishes represents an acceptance that the natural ecosystem is no longer sound and intact.. In 

this case, the resident fish propagation program might raise non-native fish to provide a warm-water 

fishing opportunity in the newly created reservoir as mitigation for the extinct salmon run. Thus, 

evaluation of this resident fish propagation program using an anadromous fish propagation criterion 

-- such as the degree to which a hatchery stock enhanced a native run -- would be irrelevant because 

the run is extinct and thus cannot be enhanced. Secondly, life histories and migratory patterns of 

anadromous salmonids and resident fish in the basin can be completely different. For example, an 

anadromous salmonid propagation evaluation criterion of percent adult return (i.e. return to the rack) 

45
would be an irrelevant measure of the success of a resident fish program with a goal of establishing a 

put-and-take recreational fishery. Rather, in this resident fish example, perhaps a measure of angler 

satisfaction, or return to the creel would serve as an appropriate evaluation criteria. It is extremely 

important, therefore, that serious consideration is given to developing biologically meaningful and 

accurately measurable evaluation criteria to evaluate the success of resident fish propagation 

programs throughout the basin with the same rigor as applied to anadromous salmonid programs.

VI. Synthesis of Artificial Production Reviews

Differing points of view on the value and importance of artificial production are not lacking in 

fisheries science. Hatchery production has been the center of controversy as long as hatcheries have 

existed on the Pacific Coast. Both the ecological and economic points of view have been debated 

without resolution because the conclusions usually reflect the preconceived perspective of the 

reviewers. One side of the issue is dominated by practitioners who base their point of view on the 

evidence of hatchery returns, but tend to ignore the ecological implications of hatchery fish on 

endemic stocks or the larger biological community. The other side is dominated by scientists who 

base their point of view on theory and ecological principles, in spite of societal benefits of a 

propagated fishery. 

Scientists and fish culturists should be concerned about the findings of three independent scientific 

panels that concluded hatcheries have generally failed to meet their objectives. The findings of those 

panels are discussed in detail later in this report. As general background, it is informative to 

examine the reviews on the subject and get a better appreciation of the issues confronting the use of 

artificial production. It is important to keep in mind, however, that artificial production in these 

assessments is narrowly defined around the standard production hatchery where tray incubators and 

concrete raceways provide the artificial incubation and rearing habitat. 

A. Early Hatchery Evaluations 

It might seem that use of a major program such as hatchery production to augment and mitigate for 

loss of historical fisheries would be evaluated to determine whether it is achieving its objectives. 

However, that did not occur in the Columbia River hatchery program. Part of the explanation for 

this failure comes from the ideological rather than scientific roots of the programs (see Historical

Overview of Artificial Production). A major shortcoming of ideology-driven technology is that it is 

46
not allowed to fail. Its success is assured by ignoring the signs of failure so by the time the failure is 

recognized, great damage has usually already occurred (Dyson 1997). This observation clearly 

describes the Columbia River hatchery program prior to 1960, and to a lesser extent after 1960 as 

well. 

During their first 80 years of hatchery operation, claims of success for the program were based on 

short-term correlations; evidence that was weak at best, or on no evidence at all. Extravagant and 

undocumented claims of hatchery effectiveness characterized the early history of the program. For 

example, in 1883, George Brown Goode of the U.S. Fish Commission told the International 

Fisheries Exhibition in London, England, that the Pacific salmon fisheries in the Sacramento and 

Columbia rivers were under the complete control of fish culture (Maitland 1884). When Goode 

made that claim, the only hatchery on the Columbia River had been closed for two years (Cobb 

1930). This again illustrates the disconnect between science and the hatchery program in its early 

developmental period. 

Perhaps the first serious evaluation of the hatchery program came from Marshall McDonald, who 

succeeded Spencer Baird. He concluded: 

". . . we have relied too exclusively upon artificial propagation as a sole and adequate means for 

maintenance of our fisheries. The artificial impregnation and hatching of fish ova and the 

planting of fry have been conducted on a stupendous scale. We have been disposed to measure 

results by quantity rather than quality, to estimate our triumphs by volume rather than 

potentiality. We have paid too little attention to the necessary conditions to be fulfilled in order 

to give the largest return for a given expenditure of effort and money." (McDonald, 1894, p.15). 

McDonald raised three important concerns regarding the use of hatcheries including: 

1) a warning regarding an overdependence on hatchery production as a substitute for 

stewardship; 

2) a criticism that hatchery performance was based on the quantity of juveniles released rather 

than the quality of the adult populations; and 

3) a recommendation to evaluate the quality of the receiving waters in watersheds to be stocked 

with hatchery fish. 

47
To varying degrees all of these concerns are still valid today.

State salmon managers challenge the assertion that scientific evaluations did not exist in the early 

decades of the hatchery program. The managers point specifically to a marking experiment carried 

out from 1895-1900 (Dehart 1997). In this experiment, 5,000 chinook salmon eggs were transferred 

from the Sacramento River and incubated at the Clackamas Hatchery in the Columbia basin. The fry 

were marked by removing the adipose fin and released, and for the next several years cannery men 

recorded the appearance of these fish in their facilities. Sex and weight were determined for some of 

the fish. However, to label this experiment scientifically valid, the following would have to be 

accepted: 

1) That 5,000 chinook salmon eggs transferred from the Sacramento River and released as 

marked fry in the Clackamas River achieved a minimum 10 percent return as adults just to 

the canneries. 

2) That the majority of adults returned in their third year, a year earlier than average, and they 

were five pounds heavier than the average for the Columbia River -- one supposed three-year 

old weighed 57 pounds. 

3) That the cannery operators reliably identified the marked salmon and accurately recorded 

their weights. The fish commissioner apparently did not personally inspect the fish that the 

cannery operators claimed to be marked. 

The validity of the experiment is questionable, and the results were questioned by at least one 

contemporary biologist (Gilbert 1913). 

Other experiments relied on short-term correlations. The common practice before 1910 was to 

release juvenile salmon shortly after hatching and before they started to feed. In 1911, hatchery 

managers held a group of chinook salmon and fed them for several months before release. The catch 

increased in 1914, the year managers expected the first returns from their experiment. After five 

successive years of improved catches in the Columbia River, the Oregon Fish and Game

Commission announced the success of their experiments: 

48
"... this new method has now passed the experimental stage, and ... the Columbia River as a 

salmon producer has 'come back.' By following the present system, and adding to the capacity 

of our hatcheries, thereby increasing the output of young fish, there is no reason to doubt but 

that the annual pack can in time be built up to greater numbers than ever before known in the 

history of the industry..." (Oregon Fish and Game Commission 1919). 

Subsequent review indicated that the claims of hatchery success were premature and the increased

catch was not caused by the new methodology (Johnson 1984) and probably had little to do with 

artificial propagation. Instead, the increase in harvest from 1914 to 1920 was consistent with the 

pattern of variation in harvest for the previous 20 years (Figure 3) and probably resulted from

favorable environmental conditions. For example, the 1914 chinook salmon run into the Umatilla 

River, which had no hatchery, also increased dramatically (Van Cleve and Ting 1960), supporting 

the suggestion that the increase in harvest was a response to natural climatic fluctuations. 

In 1914, Willis Rich initiated studies of the life history of chinook salmon that had two practical 

purposes: 1) to determine the value of hatchery work; and 2) to understand the differences in early 

life history between spring and fall chinook (Rich 1920). Rich also initiated several marking 

experiments at hatcheries in the basin to test the efficiency of hatchery practices and the homing 

ability of chinook salmon (Rich and Holmes 1929). The marking experiments were a major 

improvement over earlier "evaluations," but they did not come close to the standards of experimental 

design used in later evaluations. 

Based on his observations on the timing of the migration of juvenile chinook salmon, Rich (1920) 

concluded that the release of sack fry should be terminated. He recommended that fry be held in the 

hatchery and released during the natural migration. He also recommended that juveniles be allowed 

to migrate out of the hatchery ponds on their own volition. 

Nationally, by the 1920s biologists were beginning to question the efficacy of fish culture during its 

first 50 years. As a result, hatchery programs came under increasing criticism (Wood 1953). Rich 

(1922) completed a statistical study of the Columbia River hatchery program discussed in the 

previous section, but that study was never published. The lack of rigorous, scientific evaluation of 

the hatchery programs for Pacific salmon led Cobb (1930) to conclude that artificial propagation 

could become a threat to the Pacific salmon fishery. Cobb was not opposed to artificial propagation, 

49
but he believed that managers had to put aside their optimism and stop relying on hatcheries alone to 

increase or maintain the fishery. 

By the 1940s, individual hatcheries were fin-clipping juvenile salmon in order to evaluate returns to 

the hatchery from routine production or to evaluate experimental hatchery practices. Often the 

experiments had too few recoveries to be conclusive. Wallis (1964) summarizes the results of many 

of those studies. 

Extended rearing in the hatcheries prompted research into the nutritional requirements of juvenile

salmon and the prevention and treatment of diseases. Through the 1950s, the development of new 

feeds, better prevention and treatment of diseases, and improved hatchery practices such as the 

optimal size and time of release (Hagger and Noble 1976) started to produce tangible results. By the 

1960s smolt-to-adult survival had increased significantly. 

In the early 1960s, Congress placed a moratorium on new hatcheries until their effectiveness was 

evaluated. In response, the National Marine Fisheries Service (NMFS) conducted a series of largescale evaluations of the contribution of chinook and coho salmon from Columbia River hatcheries to 

various fisheries in the Northeast Pacific. The 1961 through 1964 broods of juvenile fall chinook 

from 13 hatcheries in the Columbia Basin were fin clipped before release so their contribution to the 

sport and commercial fisheries could be estimated. Results of the evaluation were positive. The 

benefit/cost ratio for all hatcheries combined for each of the brood years was 1961: 3.7/1; 1962: 

2.0/1; 1963: 7.2/1; and 1964: 3.8/1. The potential catch per 1,000 fish released was 1961: 6.7; 1962: 

3.1; 1963: 10.0; and 1964: 6.5. Average survival for all hatcheries combined was 0.7 percent. 

Overall, an estimated 14 percent of the fall chinook salmon caught in the sport and commercial 

fisheries from southeast Alaska to northern California originated from the Columbia River hatcheries 

(Wahle and Vreeland, 1978). 

The NMFS repeated the fall chinook evaluation with the 1978 to 1982 broods. Total survival for all 

four brood years and all facilities was 0.33 percent or about half the survival of the earlier study, 

however the benefit/cost ratio was still positive at 5.7/1. The overall contribution to the fishery was 

1.9 adults for each 1,000 juveniles released (Vreeland 1989). The NMFS used a similar approach to 

evaluate the contribution made to the West Coast fisheries by the 1965 and 1966 broods of coho 

salmon. Juvenile coho salmon from 20 hatcheries in the Columbia Basin were marked for the study. 

50
Recoveries were monitored from British Columbia to California. Coho salmon from Columbia River 

hatcheries made up about 16 percent of the total catch in the sampling area (Wahle et al. 1974). 

These evaluations were well designed and executed, but they only addressed the first question listed 

among the four criteria on determents of performance. 

B. Recent Review Summaries of Independent Panels 

Three independent scientific panels recently reviewed the use of hatcheries in Pacific salmon 

management, including the Northwest Power Planning Council’s Independent Scientific Group 

(ISG), 1996; the National Research Council (NRC), 1996; and the National Fish Hatchery Review 

Panel (NFHRP), 1994. The three panels were in general agreement on three important points: (1) In 

spite of some success, hatcheries generally failed to meet their objectives, (2) hatcheries have 

contributed to the decline of wild salmon, and (3) the region’s salmon managers have failed to 

conduct adequate monitoring and evaluation to determine if the hatchery objectives were achieved. 

These reviews conclude that over the last century, massive funding for hatcheries not only failed to 

achieve objectives, but more importantly the lack of monitoring and evaluation meant that the region 

passed up the opportunity to learn adaptively about artificial propagation of Pacific salmon (NRC 

1996). 

The individual reviews are summarized below. 

ISG – Return to the River : 

The ISG concluded that artificial production has been institutionalized in the Columbia River Basin. 

Today 80 percent of the salmon and steelhead in the basin are hatched and reared in hatcheries. From 

1981-1991, expenditures on hatcheries accounted for 40 percent of the budget for salmon 

restoration. Fifty percent of the increase in salmon production under the NPPC’s program is 

expected to come from artificial production. The historical assumption by management institutions 

was that artificial production could compensate for habitat destruction, which led to less emphasis on 

habitat protection and more emphasis on hatchery construction. More recently hatchery programs 

have been intended to augment declining natural production due in large part to habitat degradation 

throughout the basin and to maintain a supply of salmon for the fishing industry. 

In the context of the entire history of the hatchery program and salmon management in the Columbia 

River Basin, the ISG concluded that artificial production has failed to replace or mitigate lost natural 

51
production of salmonids due to habitat degradation. Since 1960, total releases from hatcheries have 

increased substantially, but the number of adult salmon entering the river has not increased. 

Furthermore, hatchery-reared fish have become the dominant portion of the run. 

It was determined that artificial production can have adverse effects on wild fish including increased 

mortality in mixed stock fisheries, genetic interactions that can cause reduced fitness of wild 

populations and loss of genetic variability, spread of disease, and increased competition with wild

fish. The ISG recommended that hatchery populations should be evaluated for evidence of 

selection, and changes in fitness or genetic diversity associated with residence in the hatchery 

environment. 

The ISG felt that new roles for artificial production need to be defined. Artificial production should 

likely have a more limited role than at present. The use and role of artificial production needs to be 

coordinated with the overall Columbia River Basin restoration goal, as well as with subbasinspecific goals. Hatcheries may need to serve as temporary refuges for endangered or critically 

depressed stocks until factors limiting their abundance can be corrected. Ideally, supplementation 

should be viewed as a small-scale and temporary strategy to boost natural production. New 

supplementation projects should follow the guidelines developed by the Regional Assessment of 

Supplementation Program (RASP). Supplementation should be used in conjunction with, but not in 

place of, habitat restoration and modification of downstream mortality factors. Supplementation 

should be approached cautiously in an experimental framework that relies on careful design, 

rigorous evaluation, and incorporates adaptive management. 

The ISG concluded that the role of artificial production in salmon restoration has to be redefined. 

Hatcheries should have a more limited role in salmon production and restoration and should be 

integrated into strategies that focus on habitat restoration, reduction of human-induced mortality, and 

conservation of existing genetic and life history diversity in natural populations. Hatcheries could 

have a useful role as temporary refuges for dwindling populations while causes of natural mortality 

are alleviated, or a temporary role in rebuilding depressed populations through supplementation. 

A comprehensive evaluation of hatchery programs in the Columbia River Basin has never been 

conducted. The ISG believes an evaluation should be undertaken and should address the following 

questions: 1) Do salmon and steelhead of hatchery origin contribute to the fisheries and/or 

52
escapement and is the economic value of that contribution greater than the cost to produce it? 2) Is 

the level of contribution consistent with the purpose or objective of the hatchery? For example if a 

hatchery is intended to replace natural production lost due to habitat degradation, this question asks 

did the hatchery, in fact, replace the lost production? 3) Do artificially produced fish add to existing 

natural production or do they replace it; i.e., does the hatchery operation generate an impact to 

natural production through mixed stock fisheries, domestication, and genetic introgression?

NRC – Upstream:

The national debate on the use of hatcheries has gone on for most of this century, but with the 

serious decline of anadromous salmonids across the nation, and hatcheries being proposed as part of 

the recovery plan, the NRC launched a review of hatchery performance, and made sweeping 

determinations on how hatcheries should be employed.

The NRC concluded that management of hatcheries has had adverse effects on natural salmon 

populations. Hatcheries can be useful as part of an integrated, comprehensive approach to restoring 

sustainable runs of salmon, but by themselves they are not an effective technical solution to the 

salmon problem. Hatcheries are not a proven technology for achieving sustained increases in adult 

production. Indeed, their use often has contributed to the damage of wild runs. In many areas, there 

is reason to question whether hatcheries can sustain long-term yield because they can lead to loss of 

population and genetic diversity. It is unlikely that hatcheries can make up for declines in 

abundance caused by fishing, habitat loss, etc., over the long term. Hatcheries might be useful as 

short-term aids to a population in immediate trouble while long-term, sustainable solutions are being 

developed. Such a new mission for hatcheries – as a temporary aid in rehabilitating natural 

populations – could be important in reversing past damage from hatcheries as well as from other 

causes. 

The NRC proposed that the intent of hatchery operations should be changed from that of making up 

for losses of juvenile fish production and for increasing catches of adults. They should be viewed 

instead as part of a bioregional plan for protecting or rebuilding salmon populations and should be 

used only when they will not cause harm to natural populations. Hatcheries should be considered an 

experimental treatment in an integrated, regional rebuilding program, and they should be evaluated 

accordingly. Great care should be taken to minimize their known and potential adverse effects on 

genetic structure of metapopulations and on the ecological capacities of streams and the ocean. 

53
Special care needs to be taken to avoid transplanting hatchery fish to regions in which naturally 

spawning fish are genetically different. The aim of hatcheries should be to assist recovery and 

opportunity for genetic expression of wild populations, not to maximize catch in the near term. Only

when it is clear that hatchery production does not harm wild fish should the use of hatcheries be 

considered for augmenting catches. Hatcheries should be audited rigorously. Any hatchery that 

“mines” brood stock from mixed wild and natural escapements should be a candidate for immediate 

closure. It is useful for all hatchery fish to be identifiable. Marking hatchery fish externally is 

particularly important when fishers and managers need to distinguish between hatchery and wild 

fish. 

It was concluded that current hatchery practices do not operate within a coherent strategy based on 

the genetic structure of salmon populations. A number of hatcheries operate without appropriate 

genetic guidance from an explicit conservation policy. Consistency and coordination of practices 

across hatcheries that affect the same or interacting demes and metapopulations is generally lacking. 

All hatchery programs should adopt a genetic conservation goal of maintaining genetic diversity 

among and within both hatchery and naturally spawning populations. Hatchery practices that affect 

straying – genetic interaction between local wild fish and hatchery-produced fish – should be closely 

examined for consistency with regional efforts. 

The NRC recommended that hatcheries should be dismantled, revised, or reprogrammed if they 

interfere with a comprehensive rehabilitation strategy designed to rebuild natural populations of 

sustainable anadromous salmon. Hatcheries should be tested for their ability to rehabilitate 

populations whose natural regenerative potential is constrained severely by both short- and longterm limitations on rehabilitation of freshwater habitats. Hatcheries should be excluded or phased 

out from regions where the prognosis for freshwater habitat rehabilitation is much higher. 

The NRC also recommended that decision-making about uses of hatcheries should occur within the 

larger context of the region where the watersheds are located and should include a focus on the 

whole watershed, rather than only on the fish. Coordination should be improved among all 

hatcheries – release timing, scale of releases, operating practices, and monitoring and evaluation of 

individual and cumulative hatchery effects, including a coast-wide database and wild fish 

proportions and numbers. Hatcheries should be part of an experimental treatment within an 

adaptively managed program in some regions but not in others. 

54
NFHRP: 

The Director of the U.S. Fish and Wildlife Service (USFWS) asked the National Fish and Wildlife 

Foundation to conduct a review and assessment of the USFWS federal fish hatchery program and 

make recommendations for the future role of the National Fish Hatchery Program in ecosystem

management of fisheries resources. The National Fish and Wildlife Foundation (through a contract 

to the Conservation Fund) convened a panel of 16 fisheries and conservation authorities (NFHRP) to 

conduct the review. 

The Panel felt the National Fish Hatchery Program needed a fundamental redirection of programs, 

personnel and facilities toward supporting ecosystem management whether it relates to restoring 

depleted anadromous populations or the recovery of ESA-listed stocks. A well-defined national 

fisheries program with definite goals, objectives, implementation and evaluation strategies did not 

exist. 

The Panel identified habitat alteration or destruction as the primary causes of decline and noted that 

resource managers have responded to declines in returning salmon by requesting hatcheries to 

produce more fish for release, with very little assessment or evaluation. The assumption that more 

fish would solve the problem of decline had very little evaluation to verify the approach. 

Mitigation based solely on hatchery production (involving 38 of the 78 USFWS hatcheries) has 

failed to halt population declines; therefore, as a better alternative, habitat protection and restoration 

were believed to be the key to survival of native fish stocks. 

The Panel concluded its report by proposing a new role for hatcheries and a new approach to 

resource management in which hatcheries would serve a support function to managers, producing 

only those species, stocks, strains, races and numbers that were compatible with ecosystem

management plans and specifically identified in those plans. Fisheries management plans should 

include genetic and ecological assessments of native stocks and strains in any ecosystem subject to 

new fishery resource projects for restoration or enhancement or for the stocking of newly created 

waters. This should be followed by careful risk assessment. Restoration of sport fishing in altered or 

newly created waters should involve the use of propagated fish of the most similar native stock 

known to inhabit the same type of habitats. Before any hatchery fish are planted, a comprehensive 

55
assessment, analysis, and a fisheries management plan should have been completed to address 

concerns about native stocks. Similarly, in efforts to restore depleted populations or to re-establish 

new populations, resource managers should avoid stocking any non-native strains or species. 

It is apparent that considerable attention has been given to evaluation of anadromous hatchery 

programs. However, no comprehensive reviews of basinwide resident fish artificial propagation 

have been undertaken. The situation is largely due to the fact that resident fish hatcheries are 

generally successful in fulfilling their mission to supply fish for management purposes where 

migratory success or return performance have not been relevant criteria. However, their absence 

from hatchery evaluations, especially when resident fish are applied in such a diversity of 

circumstances, leaves a void when addressing the role of resident hatchery fish in ecosystem

management, or even the economic benefit of resident fish hatchery programs. This situation 

illustrates the need to include resident fish hatcheries in the overall hatchery evaluation and to 

develop appropriate resident fish hatchery evaluation criteria. 

State agency and tribal interests in the basin have participated in other reviews or assessments of 

artificial production. These have been directed at review, determination of research needs, 

production alternatives, program coordination and monitoring of artificial production. These 

assessments are based on the experience of practitioners that not only have great confidence in the 

potential of artificial production, but have developed standards that are expected to improve the 

performance of hatcheries. In many cases these documents provide a substantive foundation on 

which such work can proceed. Below we discuss two of these assessments, the Regional 

Assessment of Supplementation Project and the Integrated Hatchery Operations Team. 

RASP: The Regional Assessment of Supplementation Project

In 1992, the first phase of the Regional Assessment of Supplementation Project (RASP) was 

completed. It provided an overview of ongoing and planned activities associated with 

supplementation, and development of a model to estimate potential benefits and risks from

supplementation. It also was a plan to coordinate research and monitoring on supplementation in the 

Basin. It provided guidelines for the use of supplementation aimed at minimizing negative genetic 

and ecological interactions between wild and hatchery-produced fish. 

56
At the core of the RASP guidelines are five steps that address planning, implementation and 

evaluation of restoration projects. Although specific instructions for carrying out each of the steps 

are provided, RASP recommends that within the framework of the five steps, each project should 

develop specific details and approaches that are appropriate for the local situation. The five basic 

steps contained in RASP are: 

1. Objectives: 

Project objectives should be clearly stated and contain measurable end points, i.e., criteria for 

determining when the project objectives have been achieved. The objective should also include 

consideration of resource quality as well as quantity. Resource quantity refers to a target number of 

fish -- the number of salmon harvested in the sport fishery, the number of salmon escaping to spawn 

in a stream, or the number of smolts migrating out of a stream into the ocean. Resource quality 

refers to such things as the distribution of the catch by area or fishery, stock selection or run timing. 

For example, if the objective were to establish a fishery on the returns from artificially propagated 

fish, it may be desirable to specify in the objective an extended run timing to spread the fishery over 

a longer time interval. This specification would place conditions on the quality of the eggs used. 

They would have to come from all segments of the spawning migration and from an appropriate 

stock from the genetic standpoint that exhibited normal run timing. 

2. Analysis of Limiting Factors: 

 RASP recommended comparing what is known about the character of healthy habitat and salmon 

populations in a target stream with current conditions in the stream and the populations to be 

enhanced. This comparison is used to identify potential limiting factors, and to identify the specific 

problem the project is or should be trying to overcome. 

3. Treatment: 

This step simply identifies the activity or restoration tool selected to overcome the problem

identified in the previous step. The treatment must be consistent with the objective as well as the 

problem. It is important that the right tool be selected to do the job described in steps one and two. 

Treatments might include artificial propagation in one or more of its various forms, habitat 

improvement, public education, or political activities to change statutes or regulations. 

4. Risk Analysis: 

57
All salmon restoration projects contain uncertainties that should be identified during the planning 

phase. Uncertainties are like red warning flags -- they identify the potential risks that must be 

addressed if the project is to achieve success and avoid unintended problems. Risk analysis helps 

establish the priorities for monitoring and evaluation. 

5. Monitoring and Evaluation: 

Part of the reason salmon stocks are in trouble today is that past restoration efforts were approached 

with so much optimism, especially when hatcheries were involved, that monitoring and evaluation 

were considered unnecessary. Many programs that produced little or no benefits or were detrimental 

were continued for several years or decades. The region and the salmon can no longer afford longterm investments in unproductive or counterproductive programs. It is critical to determine whether 

specific restoration activities are working and, if not, adjust them to improve the chances of success. 

IHOT: Integrated Hatchery Operations Team

Hatcheries in the Columbia basin are funded, co-managed, and operated by many different entities 

for many different purposes. The NPPC’s Strategy for Salmon (NPPC 1992) recognized the 

potential for hatcheries to help rebuild salmon production but also the need to improve the coordination and operation of these facilities. To address these latter needs, the Council called for the 

development of the Integrated Hatchery Operations Team (IHOT) to develop hatchery policies for 

operating within the Basin. The preface of the IHOT report (1994) clearly states the content and 

intent of this report: 

“The hatchery policies presented in this manual are not intended to establish production 

priorities. Rather, the intent is to guide hatchery operations once production numbers are 

established. Hatchery operations discussed in this report include broodstock collection, 

spawning, incubation of eggs, fish rearing and feeding, fish release, equipment maintenance 

and operations, and personnel training. Decisions regarding production priorities must be 

provided by fishery managers through a comprehensive plan that addresses both natural and 

hatchery fish production.” 

The IHOT report presents regional policies for hatchery coordination, performance standards, fish 

health, ecological interactions and genetics. The policies and procedures outlined were a substantive 

contribution undertaken by the hatchery management agencies to standardize artificial production 

58
operations to maximize production performance and minimize impacts on naturally producing stocks 

in the basin. Because records on hatchery production and operations are maintained by all basin 

hatcheries under their own state, federal and tribal programs, the implementation and monitoring of 

these IHOT parameters (see discussion below) at the different hatcheries can be initiated within the 

present management structure, and will be a valuable contribution to hatchery assessment in the 

future. 

The IHOT report is not a hatchery assessment or review of their technical merit, rather it is an 

operations manual. The report is notable for establishing regional policy statements and goals that 

members agreed to pursue in operating the region’s hatcheries. The actual procedures and standards 

to be used to guide operations were identified, and performance measures described how compliance 

would be monitored and evaluated. The report states that it includes performance standards 

encompassing all aspects of hatchery facilities and operations that influence the hatchery’s “final 

product." The product is defined as “a fish that has minimal impact on wild stocks and also 

contributes to harvest opportunities and natural spawning populations.” (pg. 19). However, whether 

the “final product” achieves this goal is not assessed. 

The report further recognizes: 

• that many of the facilities in the basin originally were developed to meet management objectives 

that are different from objectives today; 

• that hatchery production may be established by several existing authorizations and agreements; 

• that production goals for hatcheries have been established through a variety of fish management, 

political, and administrative processes; and 

• that environmental conditions (e.g., ocean conditions and in-river habitats) outside of hatcheries 

have “overriding influences that control production capacity.” 

Consequently, IHOT addresses operational guidelines for handling, rearing, and releasing of fish 

(i.e., issues within the control of facility managers) and notes that these will change over time in 

response to new management objectives. 

The report proceeds to provide detailed recommendations on facility environmental conditions, and 

general guidelines for hatchery operations, and fish health policies and procedures. Chapters on 

59
ecological interactions and genetic policies are much less like a cookbook than the previous chapters 

(indicative of the state of knowledge in these topics), and IHOT defers to the involvement of experts 

to assist in these areas. However, the policy statements for these greatly overstate our knowledge 

and our capabilities to monitor potential impacts. For example, the policy on ecological interactions 

states “that artificial propagation programs will be designed and implemented to minimize ecological

interactions that adversely affect the productivity of aquatic ecosystems”(emphasis added). The 

genetic policy states that these programs will “maintain adequate genetic variation and fitness in 

populations and protect the biological diversity of wild, natural, and cultured anadromous salmonid 

populations” (emphasis added). IHOT provides some general guidelines expected to be consistent 

with these policies and to minimize impacts, but the basin lacks evidence that these controls are 

effective or adequate. It is a notable development, however, that the IHOT members acknowledged 

an increasing need to incorporate ecological and genetic guidelines in the management and culture of 

hatchery salmonids. 

In reviewing the role of hatcheries in the Columbia Basin, the IHOT report and associated hatchery 

audits demonstrates a commitment to consistent operational procedures with an aim to improving 

production efficiency. The report is clearly able to draw on extensive research and experience in 

fish culture and fish health. However, there is an equally clear need for monitoring and assessment 

of the ecological and genetic guidelines. 

The IHOT report infers an important message: that hatchery staff should be accountable for the 

quality of cultured fish, but policy makers must clearly communicate objectives and resource 

managers must advise how to integrate hatchery and natural production. The parties to IHOT agreed 

to a policy to coordinate the operation of fish hatchery programs to meet basinwide resource 

management needs. The IHOT report does not consider hatcheries at this programmatic level, nor 

does it address the adequacy of monitoring and assessment programs to achieve this integration. 

In 1995, the draft Programmatic Environmental Impact Statement on Impacts of Artificial Salmon 

and Steelhead Production Strategies in the Columbia River Basin was prepared for federal hatchery 

programs by the Columbia Basin Fish and Wildlife Authority. This was a document directed at 

alternatives for how hatcheries might be used and the effects that alternative strategies would have 

on overall production, stock diversity, and social/economic conditions associated with the basin. 

60
In 1998, a summary of independent audits of salmonid hatcheries based on IHOT performance 

measures was compiled for the Northwest Power Planning Council by Sampsel Consulting Services. 

Following IHOT guidelines, the summary reviewed 20 Oregon Department of Fish and Wildlife 

hatcheries, seven Idaho Department of Fish and Game hatcheries, 20 Washington State Department 

of Fish and Wildlife hatcheries, and 12 U.S. Fish and Wildlife Service hatcheries. Considerable 

detail was provided on facility descriptions and protocols for hatchery operating procedures, with 

limited production and cost data. Unfortunately and curiously, no overall assessment of these audits 

has been conducted. 

Assessment of hatchery performance has also been conducted by agencies with regard to certain 

hatchery programs over the years that provided valuable insights on hatchery fish behavior after 

release to the stream environment. An example of such assessment the annual report of Mitchell 

Act Hatcheries in 1996, by Ashbrook, Byrne, and Fuss. Stock characteristics in the hatchery, 

migratory behavior of hatchery fish and evaluation of hatchery practices from selective breeding to 

hatchery habitat were assessed. The results of this work allowed operations to be altered to change 

the quality of the product released. 

C. Relevance of Past Assessments to the Present Task 

The history and evaluations in the preceding sections are valuable to our understanding of the origins 

of artificial production on the Pacific Coast and the Columbia River. It should be clear that to 

proceed with artificial production “as usual” would be poorly advised. Even the assumptions basic 

to the hatchery program that have carried over from the early years need to be modified in light of 

what is known about specific life history requirements of the different salmonid species that are 

managed. 

The most compelling development point, however, is the change in the general philosophy on 

resource management that hatchery programs must now address. The human influence on the 

environment is so pervasive and domineering that resources no longer can demonstrate the resiliency 

and forgiveness of abuse that was so common in past exploitation. The ecosystem approach to 

fisheries management is not so much a new paradigm as it is a necessity for the preservation of the 

fisheries resources. Fish species and their component populations cannot sustain themselves apart 

from the habitat they evolved with. Ecosystem management is not a revolutionary approach, it is the 

exercise of common sense to curb the loss of natural productivity and to maintain the health of

61
fisheries resources for public use under the concept of the “normative ecosystem” (Williams et al., in 

press). 

Regarding the three recent independent reviews of hatcheries by the ISG, NRC, and NFHRP, it is 

noteworthy that apart from primary agreement among reviews that artificial production had 

generally failed to meet its objective, that it imparted adverse effects on natural populations, and that 

evaluation of performance was needed, there was further significant consensus on other issues. 

There was agreement that: 

• Supplementation needed to be linked with habitat improvements; 

• Genetic considerations needed more emphasis in hatchery programs; 

• Stock transfers and introductions of non-native species should be eliminated; 

• A new role for artificial production needed to be developed, using more experimental 

approaches, and using hatcheries as temporary refuges, rather than in long-term production 

management. 

These points of view provided insights that need to be considered in hatchery management. They 

were comprehensive enough that retracing that ground by the SRT would only be repetitive and add 

no further resolution to the problems that were identified. It is important to point out that the 

reviews were not a referendum against hatcheries, but rather a very creditable assessment of 

hatchery success in reaching their objectives and how programs should change. 

We must also recognize that the practitioners’ view was not represented on the three panels, nor was 

the view of commercial harvesters or that of the angling public, all of whom are pertinent to 

decision-making about hatchery application. University scientists dominated or were well 

represented on the review panels. The NRC committee, for example, was made up of 15 

participants, of whom 12 were associated with universities. There were no members experienced in 

hatchery production or aquaculture on the NRC panel. Even the NFHRP panel, charged to assess 

USFWS hatcheries, did not have equitable representation from hatchery production management. 

Moreover, the reviews were largely based on ecological theory, biological principles, and some

empirical evidence, but little rigorous analysis of actual data was undertaken. This is not a criticism

of the process, because it is important that the understanding and implications of hatchery production 

be grounded in the basic science relevant to the subject. This is necessary regardless of how 

62
successful hatchery programs are or can become. To adequately manage the resource on a sustained 

basis, there can be no compromise with the requirements of biological processes. Whether society

decides that other priorities supersede the need to maintain a specific population or a habitat is 

another issue, but if fisheries management is serious about building naturally sustained production, 

science must be the basis of any approach. 

In the agency and tribal hatchery assessments such as RASP and IHOT, the practitioners' viewpoint 

and the value of their experience was acknowledged as important to improved effectiveness of basin 

hatchery programs. The forthcoming science-based SRT recommendations serve as an independent 

confirmation of IHOT’s policies, and show that the SRT is addressing elements pertinent to the 

interests of artificial production. 

 

The RASP effort provided an important overview and also a model for evaluating supplementation 

in the second phase of the SRT review. The IHOT program primarily was oriented toward 

operations, and again is most applicable to the second phase of the phase of the independent 

assessment. However, because both the RASP and IHOT efforts did not conduct actual hatchery 

performance evaluations, their primary contribution will be the use of their monitoring protocols. 

Hatchery compliance with the operating protocol will be one criterion of the SRT assessment 

procedure. 

VII. Impacts Associated with Artificial Production

A. Background 

As apparent from the historical overview, Columbia basin hatchery programs have been motivated 

by several goals, with the most recent perhaps incompatible with those of previous years. 

Attainment of some goals may even be considered detrimental to others, and not merely because of

competition for programmatic resources, but because of conflicting outcomes. 

The practical science of hatchery management is more than 100 years old. During that time hatchery 

technology has progressed to the point that the success rate of the "hatchery phase" in the life cycle 

of salmon and steelhead is very high. In fact, it is expected that a hatchery program will produce 

more smolts per spawner than natural production. The magnitude of this relative advantage is on the 

order of 10-fold, but this advantage is restricted to the hatchery phase. It is quite a different story 

63
when considering success in the post-release phase of the life cycle. Hatchery fish experience 

substantially less survival success in the wild. This is another issue of concern in the present 

assessment. In particular, what is the relative survival of the hatchery-bred fish, their reproductive 

ability, their ecological costs, and their genetic impacts on wild fish. 

In nearly all cases, when hatchery production rationale is assessed under ecological, genetic and 

evolutionary theory, the result is unequivocally negative, but of an unknown magnitude. There are 

some limited experimental data, generally from other taxa and in specific situations, that 

demonstrates the mechanisms that underlie theory. But relevant empirical information related to 

salmonids is generally anecdotal, lacking in adequate controls, and insufficient in quantity to be 

conclusive. Thus, while we are confident that such mechanisms can apply to hatchery-produced 

salmonids, there is limited empirical evidence on hatchery impacts in the Columbia basin. Although 

some are tempted to attribute the decline of wild stocks in the basin to interaction with hatchery fish, 

as well as blaming the poor success of hatchery fish on hatchery practices, such evidence, at best, is 

indirect and neglectful of the other major environmental impacts in the system. The task of making 

linkages is a formidable one, but necessary in the fair resolution of hatchery assessment. 

B. Risk Management 

In addressing the various impacts of artificial production, it is worthwhile to first think about the 

risks associated with hatchery propagation and conflicting outcomes. To address this problem, risk 

management is an option that needs to be considered, but this may prove ineffective unless the goals 

are ranked so that priorities can be established to adopt measures that address the resolution of 

competing risks. 

1. Risks associated with failure and success:

Originally, the goal of anadromous and resident hatchery programs was production for harvest; so 

the measure of success was the number of returning harvestable adults of hatchery origin. However, 

in actual practice over the years, and perhaps as a matter of convenience, hatcheries tended to report 

their performance in terms of numbers of smolts released rather than adults returning, with the 

assumption that adult return responsiveness was in proportion. The problem with this criterion is 

that the rate of adult return for the number of smolts released varies enormously from hatchery to 

hatchery and from year to year, leaving smolt production actually an unreliable indicator of expected 

harvest. Concentrating on smolt production and not adult return diverts attention from the central 

64
issue and results in the risk of not succeeding in reaching the harvest goal, or the risk of increasing 

failure. One component of the present review, therefore, is to assess the effectiveness of hatcheries in 

meeting production goals for harvest, attempting to find patterns that might account for the success 

of some and the failure of others. 

Unfortunately, with the passage of time native runs of Columbia basin salmon have declined to such 

low levels that local extinctions have taken place, and many other populations currently are at risk. 

In this new era of concern for wild fish, the question naturally arises whether the operation of 

hatcheries is a contributing factor in the decline. In addition to the pessimism raised about even new 

state-of-the-art production hatcheries, these concerns also apply to supplementation operations as 

well as to captive brood stock programs. Ironically, there are some plausible scenarios in which the 

greater the success of the hatcheries in producing harvestable fish under the original set of goals, the 

greater the damage they would cause to the affected wild stocks that are the focus of new goals 

consistent with ecological health. These are the risks of success. Accordingly, the second 

component of the present review is to assess the magnitudes and likelihood of the various negative 

effects that hatchery operations might have on wild stocks. 

2. Risk Analysis and Risk Management:

Fishery scientists must deal with two major factors in making decisions about how to assess and 

manage risks of hatcheries: (1) the uncertainty in predicting success or failure and (2) the potential 

conflicts between multiple attributes of success. One major attribute of success is the increase of 

fish for harvest; another is the impact on wild stocks. 

Depending on how fisheries managers and the public value the probability of success in terms of 

producing fish for harvest, the annual investment in the hatchery system might be considered 

worthwhile. There is a probability that this investment will deliver a return in harvestable fish, and a 

probability that it will not, in which case the odds may justify making the investment. Evidence 

demonstrating that hatcheries contribute to harvest continues to stimulate interest in the use of

hatcheries for harvest augmentation and mitigation. 

At the same time, it is probable that anadromous and resident hatchery fish may have negative 

impacts on wild stocks, which can occur even when hatcheries are managed for supplementation or 

recovery of wild stocks. Negative effects could overwhelm the positive effects of increased survival 

65
in the hatchery during the wild phase of the life cycle. Here, the gamble is on wild stock recovery. 

Managers must not only assess biological uncertainties but also the trade-offs. In a recovery 

program, balancing may involve the probability of decreasing the risk of extinction during the 

hatchery phase versus the probability of increasing mortality during the wild phase of the life cycle. 

On a broader scale, managers must take into account both the harvest goals and goals to protect wild 

stocks. However, from a strictly ecological perspective to preserve and recover wild fish, there can 

be no such compromise. 

The critical uncertainties that dominate decision making are amenable to empirical resolution if the 

right things are measured in a controlled, systematic, and powerful experimental design. Getting the 

information needed to answer hard questions would mean a major reorganization of how hatchery 

programs are conducted, including interim changes and re-prioritization of hatchery production 

goals. Hatchery research, focusing on programmed study plans around appropriate experiments to 

quantify the effects of hatcheries and hatchery practices, would need to be the initial priority. The 

long-term priority would be to return to production goals with management and technologies 

reconditioned to maximize the benefits of artificial production in a manner that complements the 

ecological health of the system. 

C. Management Impacts on Artificial Production Effectiveness 

Although controversy about the effectiveness and impact of anadromous fish hatcheries has existed 

since hatcheries first appeared on the Columbia River, there needs to be a distinction in the object 

and substance of such controversy between those factors associated with hatchery technology and 

those associated with hatchery management. Hatchery technology occurs in many different forms, 

from juvenile rearing on formulated diets in concrete raceways to unfed fry releases from incubation 

in artificial substrate. The chinook hatchery on Sooes River, Washington; pink salmon hatcheries in 

Prince William Sound, Alaska; and the Weaver Creek sockeye spawning channel in British 

Columbia, are examples of successful hatchery programs resulting in significant enlargement of their 

respective salmon populations. In contrast, and yet with similar technology, sockeye production at 

the Leavenworth hatchery on Icicle Creek, Washington; coho and chinook production at Grays River 

hatchery on the lower Columbia River; and the Priest Rapids chinook spawning channel in the midColumbia, are examples of hatchery programs that have demonstrated no success, and may have had 

negative impacts on returns. The point is that hatchery propagation takes many different forms, and 

each can demonstrate highly variable performance, even when the same technology is used. Most 

66
certainly, present technology can be improved, and advancements associated with reduced fish 

density, natural-type habitat, and measures to reduce conditioning of fish to circumstances associated 

with culture operations offer promise of producing fish more similar in behavior and performance 

with that of wild fish. 

However, the overriding influence on hatchery performance, and the basis of the long-term

controversy, is related more to hatchery management practices of the fisheries agencies than to fish 

culture practices. Variability in hatchery performance is not so much related to technology as it is to 

the manner in which that technology has been applied. The consistent oversight in hatchery 

propagation is that management has not been careful to provide for the biological needs of the young 

salmon after release to the natural environment. Hatcheries are generally managed from the central 

office, well displaced from the fish and the streams being stocked, with little appreciation of the fact 

that these fish must integrate into a very complex environmental system. A disregard for stock 

structure and the compatibility between genetic attributes of populations and the environment 

associated with their natal systems has generally characterized hatchery management policy in the 

past. Moreover, objectives such as producing the maximum number of smolts possible with the flow 

available, and fish release programming based on space needs among competing species or year 

classes, contributed significantly to poor quality of fish and negative impacts on fish in the receiving 

environment. More recently, concern about these issues has altered some hatchery operations in an 

attempt to address problems with fish quality and wild/hatchery fish interaction. The record, 

however, is dominated by former management practices, many of which are still represented among 

Columbia River hatcheries. 

The compelling issue in assessing Columbia basin anadromous and resident hatcheries is not so 

much technology, such as whether raceways should be covered or the value of training on artificial 

diets, but management policy. That is a very different matter. Management policy dictates the 

manner in which hatcheries are employed. Management policy affects what genetic stocks are used, 

the breeding protocol, and where and in what numbers hatchery fish are planted. Management 

policy is what motivates knowing the status of the endemic stock where hatchery fish are planted, 

making sure the genetics are complementary, and knowing the carrying capacity of the target 

streams. Technology can help meet artificial production objectives, such as ensuring compatibility 

with native stocks, but management must assure that it is applied. The impact of management on 

the application of artificial production is the overwhelming and decisive factor that determines the 

67
effectiveness of hatchery programs. Good management is the key to successful integration of 

hatcheries into a functioning and dynamic ecosystem. 

D. Genetic Impacts of Artificial Production 

Better understanding of nutrition, disease, stress, and water quality has given aquaculturists 

increasing control over the unpredictable nature of raising fish. Only recently, however, have 

salmon aquaculturists become aware of genetic concerns. Artificial production can lead to unwanted 

or unanticipated genetic changes in wild and hatchery populations. These changes are a concern 

because the productivity and resiliency of populations to environmental change depend on the 

genetic diversity they contain. Unlike disease or nutritional problems, which can be controlled 

nearly immediately, the impacts of unwanted genetic changes can affect productivity for many years. 

In recent years, a variety of authors have cataloged the potential genetic impacts of artificial 

production (Hindar et al., 1991; Waples, 1991; Busack and Currens, 1995; Campton ,1995; Waples, 

1995; Allendorf and Waples, 1996). These impacts can be classified into four major types: (1) 

extinction, (2) loss of within-population genetic variability, (3) loss of among-population variability, 

and (4) domestication (Busack and Currens, 1995). The impacts are not necessarily independent. 

For example, domestication -- or loss of fitness in the wild of a population adapted to a captive 

environment -- may also be associated with loss of genetic diversity within that population. This has 

led to increasing awareness that managing genetic impacts will require assessing the trade-offs

between the major types of impacts or between using artificial production or not (Hard et al., 1992; 

Currens and Busack, 1995). 

In this subsection, we review the evidence for genetic impacts of artificial production. For each of 

the four impacts, we ask two basic questions that are important to decision-makers: (1) What is the 

evidence that the impact occurs? and (2) What is the evidence that the effects can be managed or 

mitigated? 

1. Extinction:

Definition -- Extinction is the complete loss of a population and all its genetic information. 

Theory -- Unlike other genetic impacts, extinction is usually associated with three nongenetic causes 

of large changes in population abundance (Shaffer, 1981). These include demographic or random

changes in survival and reproductive success, fluctuations in the environment, and catastrophes. 

68
Captive environments, such as hatcheries, offer greater control over environmental variation and the 

potential for increased reproductive success. These should counter natural risks of extinction. 

Consequently, artificial propagation theoretically could reduce the short-term risk of extinction 

(Hard et al., 1992). 

 

In certain circumstances, however, hatchery programs can increase the demographic and 

catastrophic risks of extinction. Hatchery programs may mine small, natural populations if they take 

fish for brood stock but are unable to replace them. For example, hatcheries that take female salmon 

with 4,000 eggs would be mining the wild stock if they have much less than 0.05-percent egg-toadult survival. Inbreeding, a genetic phenomenon, can theoretically contribute to irreversible 

declines in abundance in very small or wild populations (Gilpin 1987). When most or all of a 

population is taken into captivity, disease, power failures, predation, and dewatering in the hatchery 

could be catastrophic. 

Evidence for Extinction -- We found evidence of conditions that suggest hatcheries could contribute 

to extinction (Flagg et al., 1995a). To date, however, there are no records of hatcheries directly 

causing the extinction of stocks. In contrast, artificial propagation has been used to reduce shortterm risk of extinction for sockeye salmon (Flagg et al. 1995b), chinook salmon (Bugert et al., 1995; 

Carmichael and Messmer, 1995; Appleby and Keown, 1995; Shiewe et al., 1997), steelhead (Brown, 

1995), white sturgeon (USFWS, 1998), and bull trout (Montana Bull Trout Scientific Group, 1996) 

and other resident salmonids (Rinne et. al., 1986; Dwyer and Rosenlund, 1988). 

 

Ability to Mitigate -- Evidence suggests that the probability of extinction caused by artificial 

production can be mitigated if the reproductive success of naturally spawning and hatchery 

spawning fish is monitored and adequate safeguards are established to prevent catastrophes in 

hatcheries. We did not conclude whether the lack of hatchery-caused extinction indicates that these 

safeguards are in place or simply a fortuitous turn of events.

2. Loss of Genetic Diversity Within Populations:

Definition -- Loss of within-population diversity is the reduction in the quantity, variety, and 

combinations of alleles in a population. It is associated with two genetic phenomena: genetic drift 

and inbreeding. Both of these are most important in small or declining populations: the smaller the 

69
effective population size, the greater the rate of inbreeding and loss of genetic information through 

genetic drift. 

Theory -- The relationship between small population size, loss of genetic diversity, and increased 

inbreeding is one of the cornerstones of theoretical population genetics. Considerable theory has 

been developed to explain the generality of this relationship (Wright, 1938; Crow and Kimura; 1970; 

Goodnight, 1987; 1988; Caballero, 1994) and its importance for short-term and long-term survival 

(Lande, 1988; Mitton, 1993; Burger and Lynch, 1995; Lande and Shannon, 1996; Lynch, 1996). In 

addition, general population genetic theories have been refined to fit the specific life histories of 

Pacific salmon (Waples, 1990a 1990b; Waples and Teel, 1990). They have also been extended to 

examine the effect of increasing natural population size through artificial production (Ryman and 

Laikre, 1991; Ryman et al., 1995). 

Evidence for Genetic Drift -- Many years of experimental work have demonstrated the relationship 

between population size and loss of genetic diversity (reviewed by Wright, 1977, Rich et al., 1979, 

Leberg, 1992) in many varieties of laboratory animals. 

Support for the theory from natural populations is less available, because fewer opportunities have 

existed to measure levels of genetic diversity as population sizes changed. Low levels of genetic 

diversity have been measured in animals that have undergone known drastic reductions in population 

size. These include elephant seals (Lehman et al., 1993), koalas (Houlden et al., 1996), prairie 

chickens (Bouzat et al., 1998a, 1998b), and chinook salmon transplanted to New Zealand (Quinn et 

al., 1996). Island populations of many different taxonomic groups, which were presumably founded 

and maintained by few individuals, also have lower levels of genetic variability than mainland 

counterparts (Frankham, 1997, 1998). Where barrier dams have fragmented the range of steelhead, 

rainbow trout that survive above barrier dams have levels of genetic diversity that are lower than 

anadromous populations and that are often comparable to small populations isolated above ancient 

barriers (Currens, in prep.). 

 

Lower levels of genetic variation in anadromous and resident hatchery stocks compared to their 

counterparts in the wild (Allendorf and Phelps, 1980; Ryman and Stahl, 1980; Vuorinen, 1984; 

Waples et al., 1990) suggest that genetic variation has been lost under some kinds of artificial 

propagation. Conditions necessary for genetic drift exist in many Pacific salmon hatcheries, and 

70
evidence is growing that it occurs (Gharrett and Shirley, 1985; Simon et al., 1986; Withler, 1988; 

Waples and Teel, 1990). Salmon aquaculture affects nearly all of the factors that theoretically 

influence genetic drift and inbreeding. These include the number and proportion of founders or 

brood stock taken from the wild, sex ratios, age-structure, and variation in family size as measured 

on adult progeny. Recent increased monitoring of genetic diversity in many hatcheries will help 

resolve this question further. 

Evidence for Inbreeding and Inbreeding Depression -- Considerable experimental evidence shows 

that inbreeding can reduce fitness (reviewed in Wright, 1977 Thornhill, 1993, Roff, 1997, Lynch and 

Walsh, 1998). Tave (1993) compiled evidence for fish, including trout and salmon, thus 

representing anadromous and resident life history forms, showing that they respond to inbreeding 

similarly to other organisms. 

In natural populations, concerns arise when estimated levels of inbreeding are comparable to 

inbreeding that led to depression in experimental environments. For example, estimates of increased 

inbreeding have been associated with reduced fitness in certain Sonoran and Mexican topminnows

(Quattro and Vrijenhoek, 1989; Vrijenhoek, 1996), white-footed mice (Jimenez et al., 1994), 

butterflies (Saccheri et al., 1998), and the evening primrose (Newman and Pilson, 1997) in natural 

environments. Frankham (1998) estimated levels of inbreeding in 210 island populations of birds, 

mammals, insects and plants and observed that based on inbreeding in laboratory studies these levels 

of inbreeding could explain the higher extinction rates on islands. 

Evidence for Loss of Fitness from Artificial Propagation -- There is little direct evidence of

significant losses of fitness from genetic drift and inbreeding associated with salmon hatcheries, and 

probably fewer investigations of this phenomenon associated with resident fish hatchery programs. 

Theory and observation, however, indicate that the ability to predict or measure the effects of fitness 

using existing tools would be limited. Consequently, such losses, if they occurred, may not have 

been detectable. First of all, enzyme or DNA markers, which have been used most often to measure 

loss of genetic variation, are not the best ones to show the effects on fitness (Lynch, 1996). No 

studies of salmon have attempted to document the loss of multilocus, adaptive genetic variation and 

its consequences on fitness as have been done for experimental animals (e.g., Bryant et al., 1986; 

Bryant and Meffert, 1991). Furthermore, logistical difficulties of maintaining a powerful, 

experimental design may prohibit many such studies (Roff, 1997). Second, changes in fitness in 

71
small populations may also reflect the confounding effects of inbreeding depression or accumulation 

of deleterious mutations. Leberg (1990), for example, observed that mosquito fish populations 

derived from small numbers of related founders grew at much slower rates than control populations. 

Similar scrutiny has not been applied to salmon hatcheries. Using evidence from fruit flies, Lynch 

(1996) argued that under some kinds of artificial propagation, the accumulation of deleterious effects 

and random genetic drift would interact to reduce fitness even in moderately large populations. This 

has not been examined in Pacific salmon. 

Theory suggests that managing brood fish number, sex ratios, and age structure can control loss of 

genetic diversity and inbreeding in hatchery populations (Falconer and Mckay, 1996). For integrated 

programs, where brood stock are taken from the wild and some hatchery fish spawn naturally, theory 

suggests that controlling loss of genetic diversity may be much more difficult (Ryman and Laikre, 

1991; Ryman et al., 1995). Logistically, controlling loss of genetic diversity and inbreeding in 

captive hatchery programs or integrated programs will be difficult. Monitoring the genetic 

parameters affecting loss of genetic diversity is also difficult. Few programs have attempted to 

directly monitor the effective breeding size of the population (Hedrick et al., 1995). Variation in 

family size, which theory shows as being critical for determining the rate at which genetic diversity 

is lost, cannot be directly estimated without a pedigree of all the fish in the population. These are 

currently unavailable and unlikely to become available in the future for most populations. 

3. Loss of Genetic Diversity Among Populations

Definition -- Loss of among-population genetic diversity is the reduction in differences in the 

quantity, variety, and combinations of alleles among populations. In artificial production situations, 

it is caused by unusually high levels of gene flow that arise when fish or eggs from different 

populations are transferred between hatcheries, when fish are stocked in non-native waters, or when 

phenotypic changes in hatchery fish cause them to stray at greater rates or to different streams than 

normal. 

Theory -- The relationship between gene flow and population differentiation is another of the 

cornerstones of evolutionary biology (reviewed in Slatkin, 1985). Mathematical models show that 

unless gene flow rates are low, differences among populations will be lost (Haldane, 1930; Wright, 

1931 1943; Hanson, 1966; Barton, 1983). Evolutionary theory predicts that loss of genetic diversity 

among populations can decrease the evolutionary potential of the species. In addition, theory 

72
indicates that extensive interbreeding of genetically differentiated populations (outbreeding) may 

lead to more immediate losses of fitness or outbreeding depression (Dobzhansky, 1948; Shields, 

1982; Templeton, 1986; Lynch, 1991). Documentation of the genetic mechanisms remains elusive 

(Lynch and Walsh, 1998). At least one model of outbreeding depression is available for salmon 

(Emlen, 1991). An important conclusion of basic theory is that some forms of outbreeding 

depression will not be predictable. Consequently, the importance of outbreeding depression may 

need to be solved empirically (Roff, 1997).

Evidence of Loss of Genetic Diversity -- Evidence of loss of genetic diversity among natural 

populations from gene flow is extensive. It is especially important in western North America, where 

extensive hatchery programs have spread cultured forms of Pacific salmon and resident trout and 

other species into watersheds where they have interbred with local populations (reviewed in Behnke, 

1992; Leary et al., 1995; Waples, 1995). Loss of genetic diversity from interbreeding with 

introduced fish has been inferred for populations of the same species (Allendorf et al., 1980; 

Campton and Johnston, 1985; Gyllensten et al., 1985; Reisenbichler and Phelps, 1989; Currens et al., 

1990, 1997a; Forbes and Allendorf, 1991; Reisenbichler et al., 1992; Williams et al., 1996, 1997; 

Currens, 1997) and different species (Busack and Gall, 1981; Leary et al., 1984; Allendorf and 

Leary, 1988). Lack of extensive interbreeding in some areas where hatchery fish have been 

introduced (Wishard et al., 1984; Currens et al., 1990; Waples, 1991; Currens, 1997) indicates that 

loss of genetic variation cannot be predicted simply from knowledge of hatchery stocking rates or 

migration. 

Evidence for Loss of Fitness -- Evidence of outbreeding depression from populations in natural 

habitats is available from studies of a variety of organisms, including certain marine crustaceans 

(Burton, 1987, 1990a, 1990b), plants (reviewed in Waser, 1993), Daphnia (Deng and Lynch, 1996), 

and fish (Leberg, 1993). Most concern about outbreeding depression in Pacific salmon is based on 

evidence that Pacific salmon are locally adapted (reviewed in Ricker, 1972, Taylor, 1991) and 

theoretical and experimental results from other animals that demonstrate that interbreeding of 

different locally adapted populations could result in outbreeding depression. Limited evidence 

suggests that outbreeding depression can occur in Pacific salmon, but rigorous experiments designed 

to detect outbreeding depression in Pacific salmon are missing from the scientific literature. 

Gharrett and Smoker (1991) reported that F2 crosses of pink salmon from odd and even-year runs 

had lower survivals and greater morphological asymmetry than F1 crosses, which is consistent with 

73
outbreeding depression. Currens et al. (1997) found that a hybrid swarm of introduced coastal 

rainbow trout and native inland rainbow trout had lower levels of resistance to a lethal disease, 

ceratomyxosis, than native populations. They attributed that to interbreeding with introduced coastal 

rainbow trout, which lacked genetic resistance to the disease. 

 

Ability to Mitigate -- Two of the three major sources of loss of genetic diversity -- transfer of fish or 

eggs from different populations between hatcheries and stocking fish in non-native waters -- can be 

mitigated by management measures such as developing local brood stocks or building fish-sorting 

barriers where marked, non-native returning adults can be removed from a population. Control of 

straying that is promoted by hatchery practices is more difficult. Although increased straying is 

correlated with a variety of hatchery practices (Quinn, 1993, 1997), modifying these practices may 

not always be easy or desirable. For example, transportation of fish to increase post-release survival 

may also increase straying (McCabe et al., 1983; Solazzi et al., 1991). Monitoring the potential loss 

of genetic diversity from straying can be accomplished with existing genetic techniques. Monitoring

potential outbreeding depression is much more difficult and probably logistically possible for only a 

few experimental situations. 

4. Domestication

Definition -- Domestication is the adaptation of a captive population to its captive environment. It 

reflects the changes in quantity, variety, and combination of alleles within a captive population or 

between a captive population and its natural complement. Selection is the primary genetic 

mechanism, although it does not occur independently of genetic drift and mutation. We include both 

intentional (artificial selection) and unintentional selection (natural selection in a new environment) 

as domestication. Others have limited domestication selection to unintentional selection (Campton, 

1995). 

Theory -- The theoretical and empirical basis for selection is the foundation of biology (reviewed by 

Bell, 1997). The main principles were described in the early part of this century (reviewed in 

Wright, 1968, 1977). The fundamental theory predicts that organisms will respond to selection 

when they have adequate genetic variation for selection to act on (measured as heritability) and 

when there is a selection differential. For over 60 years, these principles have provided the 

theoretical basis for modern plant and animal breeding programs (Lush, 1937; Falconer and Mackay, 

74
1996) and our understanding of domestication. Theory has not yet been refined to answer genetics 

questions about interbreeding of hatchery salmon and natural populations 

Evidence for Domestication -- Even before modern genetics, animal breeders recognized and 

promoted domestication. Darwin (1898) considered domestication inevitable for captive animals. 

The development of captive populations for experimental genetics in the early 1900s, however, 

provided the first documentation of the genetic mechanisms of how organisms adapt to captive 

environments (reviewed in Wright, 1977). Concern about domestication in Pacific salmonids comes 

from two sources: 

First, considerable evidence shows that many behavioral and physiological traits would respond to 

selection if selection differentials also existed. Tave (1993) compiled estimated heritabilities of 

many traits. A variety of authors have argued that strong selection differentials exist in novel, 

captive environments such as hatcheries (Doyle, 1983; Frankham et al., 1986; Kohane and Parsons, 

1988). Together, these would lead to domestication. 

Second, evidence of behavioral and physiological changes in hatchery populations compared to wild 

populations is increasing. Few data are available, however, to examine the fitness effects on a 

natural population interbreeding with hatchery fish that have undergone different levels of 

domestication. Early studies of domestication found evidence of behavioral change in captive brook 

and brown trout populations (Vincent, 1960; Green, 1964; Moyle, 1969; Bachman, 1984). More 

recently, Petersson et al. (1996) documented the change in morphology and life history of a hatchery 

strain of Atlantic salmon over 23 years. Likewise, Kallio-Nyberg and Koljonen (1997) found that 

growth rate and age of maturation in Atlantic salmon changed over several generations in a hatchery. 

In steelhead, Reisenbichler and McIntyre (1977) found that progeny of hatchery fish only two 

generations removed from the wild survived in the wild only 80 survived in the wild only 80 cent as 

well as wild fish, but in the hatchery environment hatchery fish survived better. Fleming and Gross 

(1989, 1992, 1993, 1994) and Fleming et al. (1996) documented changed behavior and decreased 

reproductive success of hatchery Atlantic salmon and coho salmon in artificial spawning channels 

compared to wild fish. Swain and Riddell (1990) concluded that greater aggressive behavior of 

juvenile hatchery coho salmon than wild fish reared under the same environment was because of 

domestication selection. Berejikian (1995), however, found that hatchery steelhead raised in the 

75
same controlled environment as their wild counterparts were more likely to be eaten by a native 

predator. Compared to naturally spawning wild steelhead in the same stream, Chilcote et al. (1986) 

and Leider et al. (1990) found that naturally spawning hatchery steelhead were about 10-30 percent 

as successful in producing surviving smolts and adult progeny as wild fish. The hatchery stock used 

in this study, however, was not native to the stream and was of mixed ancestry. Consequently, the 

reproductive success of this stock reflects more than domestication effects. 

Theory indicates that controlling domestication selection may be very difficult. Busack and Currens 

(1995) reviewed domestication and concluded that it is one of the costs of using hatcheries. The 

only way to remove domestication selection is to remove the selection differential. In practical 

terms this translates to removing the differences between the hatchery and wild environments. This 

is currently unimaginable. Hatcheries are successful because they offer a better environment in 

which early survival is greater than in the wild. It may be possible to reduce selection for key traits 

if we could identify the traits, how they correlate with fitness, and what environmental conditions led 

to selection. This knowledge is not currently available. 

E. Ecological Effects of Artificial Production: 

A healthy ecosystem is often equated with conditions that characterized river basins prior to 

encroachment of modern civilization. Ecosystems are dynamic, and any point in time is only a 

snapshot in the geophysiographic transition in environmental circumstances over time. In many 

cases, return to historical conditions is not possible even if human influences could be eliminated. 

Descriptive reconstructions of historical conditions, however, are invaluable in helping to explain 

current observations that are the outcome of past processes (Lichatowich et al., 1995). 

Contemporary ecological theory recognizes the importance of considering not only the biology of 

organisms, but also the biogeochemical processes that control the distribution and production of 

biota, and human influences on those processes (Stanford et al, in press). Such historical 

reconstructions viewed under the guidelines of ecological theory provide the descriptive lens through 

which present population structure can be discerned. 

In Return to the River (Williams et al., in press), the ISG developed a conceptual foundation for 

restoration of Columbia River salmonids in which the “normative ecosystem” was defined as a mix 

of natural and cultural features that typifies modern society. It was implicit, however, and consistent 

with ecological theory, that environmental equity in the “normative ecosystem” would have to be 

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sufficient to sustain all life stages of a diverse mixture of healthy wild anadromous salmonids, 

concurrent with cultural and economic development of water resources. The ISG stated, 

“Restoration requires detailed understanding of the interactive, biophysical attributes and processes 

that control the survival of salmonids rather than a simple accounting of numbers of fish at various 

points and time in the ecosystem." The concept of ecosystem health infers that whatever changes 

occur through man-made alterations of the river system that define the “normative ecosystem," 

maximum effort is exerted to maintain existing habitat for the full exploitation of anadromous 

salmonids. Restoration, therefore, refers to measures that enhance the natural production of native 

salmonids, even to their fullest diversity possible within the potential of the “normative ecosystem." 

The fundamental benefits and risks of artificial production rest in the ability of aquaculturists to 

isolate fish from all or part of their natural habitat and ecological processes. Since their inception, 

hatcheries have been operated as agricultural enterprises that strived for biological independence 

from one or more of the ecological processes that fish face in rivers and streams (Bottom 1997). 

Hatcheries were first used to circumvent natural ecological processes, such as predation and physical 

damage to eggs, that reduced the potential productivity. Later hatcheries were used to circumvent 

entire river reaches whose natural ecology had changed from the construction of dams or other 

human activities. Production from hatcheries was often treated as production from a super tributary 

without consideration of biological interactions. Consequently, until recently, the ecological effects 

of raising and releasing hatchery fish have had little research attention. 

It is instructional to review the evidence for ecological interactions between hatchery fish and their 

post-release environments, and in wild fish communities between hatchery and wild fish. The 

continuing decline of natural populations and listings under the federal Endangered Species Act have 

focused attention on ecological factors of decline that have been previously ignored, such as 

predation, competition, disease, and nutrient flows. In addition, the attempt to increase natural 

production through hatchery supplementation has also stimulated interest in ecological effects. As 

previously mentioned, in Return to the River the ISG developed a “normative ecosystem” concept 

for restoration and management of both wild and hatchery salmonids in Columbia River salmonids 

(Williams et al., in press). 

In salmonid ecosystems, ecological interactions are complex and occur at different levels of 

biological organization from the organism to the population to the community. In this subsection, 

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we focus on five main issues: effects on carrying capacity, competition, predation, disease, and 

behavior, while recognizing that these occur and interact at different levels of biological 

organization. 

1. Effects on carrying capacity

In this subsection, we review evidence that the number of fish released from hatcheries has exceeded 

the carrying capacity of the ocean or freshwater environments. Competition, which can occur 

among individuals as a consequence of stocking at or near the carrying capacity, is discussed in 

another section. 

Definition -- Carrying capacity is the upper limit on the steady-state population size that an 

environment can support. Carrying capacity is a function of both the populations and their 

environments. 

 

Theory -- A large body of ecological theory postulates that population growth is limited by the 

amount of available resources and the relationship between these limits and environmental variation 

(Krebs 1985). Under steady state models of population growth, as a population approaches carrying 

capacity, its growth rate is reduced to zero (Lotka 1925, Volterra 1926). This view of population 

regulation assumes that there is a deterministic relationship between the abundance of a species and 

the abundance or condition of the available resources. Abundance of populations is density 

dependent because with each additional individual fewer resources are available. Although the 

notion of a carrying capacity is conceptually useful, other theorists have suggested that population 

growth may be largely controlled by unpredictable changes in environments and resources 

(Andrewartha and Birch 1954, Strong 1986). 

A. Ocean carrying capacity impacts 

Evidence -- The effects of hatchery releases on ocean carrying capacity have been studied for coho

salmon in the Oregon Production Index (OPI). The Oregon Department of Fish and Wildlife first 

addressed the question of ocean carrying capacity relative to hatchery releases by analyzing whether 

ocean mortality of coho salmon was the result of density-dependent or density-independent factors 

(ODFW 1982). Density-dependent mortality would indicate that the capacity had been exceeded; 

density-independent mortality would indicate otherwise. 

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The results of this analysis were inconclusive, but it did stimulate other studies (Lichatowich 1993). 

Seven additional papers addressed the question of whether carrying capacity in the ocean for coho 

salmon in the OPI was limiting production. The question, however, remains unresolved. The 

studies generally analyzed the same data, but they used different analytical methods and arrived at 

different answers to the question. The strength of the conclusions varied. In general, three studies 

concluded that the evidence for density dependence was weak or nonexistent (Clark and McCarl 

1983; Nickelson and Lichatowich 1983; Nickelson 1986). Three other studies concluded there was 

evidence for density dependence or at least enough evidence for caution (McCarl and Rettig 1983; 

McGie 1983; Emlen et al. 1990). One study pointed out statistical weaknesses in Nickelson (1986) 

and cautioned managers regarding its conclusion. Studies of salmon in other ocean production areas, 

including Japanese and Russian chum (Ishida 1993), Bristol Bay sockeye (Rogers 1980), and British 

Columbia and Bristol Bay stocks of sockeye (Peterman 1984) suggest salmon densities are 

approaching capacity. As with the studies of Oregon coho salmon, however, the evidence is not 

conclusive. 

Since work on OPI coho salmon, researchers have identified patterns of changing ocean productivity 

(Ware and Thomson 1991; Beamish and Bouillion 1993; Francis and Hare 1994). This pattern of 

shifting ocean productivity suggests that the carrying capacity of the ocean, especially in specific 

areas, is also changing. If that is the case, then continuing to release large numbers of hatchery fish 

during periods of low productivity (reduced capacity) might not be the appropriate strategy 

(Beamish and Bouillion 1993). 

B. Freshwater carrying capacity impacts 

Evidence -- Research documenting an effect of hatchery fish on the freshwater carrying capacity of 

salmonid streams is largely lacking. Many fishery managers assumed that effects on carrying 

capacity depend on the time and age of release. Large releases of fry or presmolts might have 

significant ecological effects on carrying capacity because they could use limited food and cover. In 

the lower Columbia River, for example, stocking hatchery fry in excess of carrying capacity was 

identified as one of the factors leading to the collapse of wild coho populations (Flagg et al. 1995). 

The mean density of emergent, wild coho fry in lower Columbia River tributaries was estimated at 

three fry per lineal stream meter (fry/m). By comparison, hatchery fry were stocked in similar sized 

streams in Oregon at a rate of 16 fry/m and in Washington at 22 fry/m. This suggests that 

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overstocking streams could have displaced wild fry in the Lower Columbia River tributaries (Flagg

et al. 1995). The use of presmolts to supplement natural production in underseeded streams 

(supplementation) also raises the possibility that large release of hatchery fish could exceed the 

capacity of the stream habitats unless stocking levels are carefully researched and controlled. 

Determination of stocking densities for supplementation projects is complicated by the need to 

consider the existing abundance of wild fish relative to carrying capacity (Stewart and Bjornn 1990). 

In contrast, in the 1950s and 1960s many hatcheries adopted the practice of holding juveniles until 

they smolted. Smolted hatchery fish were expected to use the river only as a conduit to the sea, 

which theoretically minimized carrying capacity problems. Even where smolts are released, 

however, and expected to migrate immediately to sea, release of too many fish could exceed 

capacity of the stream. In his examination of Washington’s hatchery program for steelhead trout, 

Royal (1972) speculated on what he called a “density barrier” that could have resulted from a 

combination of competition with other species, environmental factors and poor physiological 

condition of the hatchery fish. Once the barrier was reached, increasing the number of hatchery fish 

produced little or no additional benefit. 

An indirect effect of the hatchery-harvest management strategy on freshwater carrying capacity is 

the reduction in nutrient recycling to the system from carcasses. With reduced escapement needs to 

sustain hatchery programs, harvest has been given a greater share of the return, generally associated 

with the management concept of Maximum Sustained Yield (MSY). This has not only impacted 

escapements of wild fish in mixed stock fisheries, but it has affected nutrient recruitment from

carcasses that enriched otherwise nutrient-impoverished systems. Carcasses undoubtedly were an 

important source of nutrients to freshwater systems that habitually export nutrients downstream

(Bilby, et. al. 1998) The dependence on artificial production has exaggerated the deficit in nutrient 

transfer caused by management around MSY from that historically experienced, because of even 

further limited escapements required to sustain hatchery production. Consequently, reduction of 

carcass contribution to nutrient loads in salmon spawning streams is an indirect, but significant 

ecological impact of hatchery management. 

Because managers have complete control over the number of fish released, preventing hatchery 

releases from exceeding carrying capacity of freshwater or marine environments is easy if the 

carrying capacity can be known. Determining the carrying capacities of dynamic, natural systems, 

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however, is very difficult. Attempts to adjust hatchery releases to carrying capacities must take into 

account changes in climatic patterns, habitat, and communities that can cause variation in capacity. 

The Council has had a measure in its fish and wildlife program to determine the carrying capacity of 

the Columbia River relative to the basin’s hatchery production levels (Measure 7.1G NPPC 1994). 

While work on this measure was undertaken, the measure has not been fully implemented, and 

carrying capacity has not been determined. 

2. Competition

Definition -- Competition is the negative interaction between two or more individuals that occurs 

when a necessary resource is in short supply or when demand is greater for higher-quality resources. 

Theory -- Competition is one of the fundamental ecological interactions between individuals. Many 

ecologists believe that it is the major factor determining the structure and organization of ecosystems

(Cody and Diamond 1975). The theoretical treatment of competition in the ecological literature is 

extensive and well-developed (see Krebs 1985, or a similar text for an introduction). 

Evidence -- Competition is very difficult to demonstrate (Fausch 1988). Conditions for competition 

between hatchery and wild fish may occur, however, if the hatchery fish are released before they are 

ready to migrate to sea and they residualize or remain in freshwater for an extended period of time. 

Conditions may be aggravated by differences in size or behavior between the wild and hatchery fish. 

Salmonids often form dominance hierarchies in streams, where dominant individuals defend the best 

holding or feeding areas against subordinate fishes (Fausch 1988). 

In experiments using enclosures placed in the Teanaway River, Washington, residual hatchery 

steelhead reduced the growth of wild rainbow trout but did not influence the growth of juvenile 

chinook salmon (McMichael et al. 1997). When the stocking of catchable-sized hatchery rainbow 

trout was terminated in a section of the Madison River, Montana, the biomass and numbers of the 

fall population of two-year-old brown trout increased by 160 percent and the number of wild 

rainbow trout increased by 868 percent. The impact of stocking may have been caused by the 

disruption of the existing social structure in the wild population (Vincent 1987). 

In an attempt to supplement underseeded coastal streams in Oregon, ODFW stocked some streams 

with coho salmon of hatchery origin. They left some streams unstocked as controls. The total 

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summer density of juveniles increased by 41 percent in the stocked streams. However, 44 percent of 

the wild juveniles in those streams were replaced by the hatchery presmolts. Nickelson et al. (1986) 

attributed the displacement of wild fish to the larger size of the hatchery presmolts at the time of 

stocking. 

An important goal of management programs that make use of hatcheries should be to integrate the 

natural and artificial production systems (Lichatowich and McIntyre 1987). Hatchery fish should not 

replace existing wild fish. Such integration requires knowledge of the natural production system. 

Once obtained, it has to be explicitly used to plan and implement the hatchery program. Follow-up 

monitoring is critical. This approach is not impossible, but it would be difficult to implement, and at 

the present time it is the exception and not the rule in hatchery management. 

3. Predation:

Definition -- Predation is an ecological interaction where one individual becomes a food source for 

another. Predation is one of the fundamental ecological interactions observed between many 

species. The theoretical treatment of predation in the ecological literature is extensive and welldeveloped (see Krebs 1985, or a similar text for an introduction). 

Evidence -- Under different scenarios, hatchery salmonids can be predators or prey. Predation of 

one salmonid on another can be an important source of mortality. Hatchery fish released at a large 

size are potential predators on smaller wild salmonids (Stewart and Bjornn 1990). Parker (1971) 

observed that predation by coho salmon accounted for a large fraction of early sea mortality in chum

and pink salmon. If a predator such as coho salmon is enhanced through artificial propagation it 

could increase predation and cause the decline of other important salmonid. Johnson (1972) 

observed that chum salmon returns to hatchery racks was inversely related to hatchery coho 

production in Puget Sound. Although his study did not show a cause-and-effect relationship, 

Johnson (1972) concluded that managers should be concerned about the effects of the hatchery coho 

salmon program on the total production of chum. Stewart and Bjornn (1990) cited a paper by Sholes 

and Hallock (1979) that reported heavy predation on wild steelhead and chinook fry by larger 

yearling chinook salmon stocked into the Feather River, California. 

Rearing in artificial environments can make hatchery fish more vulnerable to predation than wild 

salmonids (Olla et al. 1998). Hatchery fish released at a small size are vulnerable to predation by 

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other larger salmonids or other non-salmonid fishes. In addition, hatchery fish may lack appropriate 

behaviors, perhaps from lack of prior exposure to predation, and may undergo secondary stresses 

such as disease (Stewart and Bjornn 1990), which may make them more vulnerable to predation. 

White et al. (1995) speculated that this may explain the poor post-stocking survival of hatchery fish. 

For example, feeding salmonids at or near the surface of the hatchery pond gives them a surface 

orientation that can make them more vulnerable to avian predation. Disease infection may also 

enhance the vulnerability of salmonids to predation (Mesa et al. 1998). 

Habitat modification that removes cover, modifies temperature and obstructs passage may increase 

the vulnerability of hatchery fish to predation (Spence et al. 1996). Habitat alteration may also 

enhance the predator population and lead to greater mortality. For example, the creation of Rice 

Island in the lower Columbia River from the disposal of dredge spoils created habitat for Caspian 

terns. The tern colony on Rice Island has grown dramatically and is now the largest in North 

America. The terns may be consuming between 5 and 20 million juvenile salmonids annually 

(ODFW 1998). The recovery of PIT tags on Rice Island suggests that hatchery fish may be more 

vulnerable than wild fish to predation by terns (Roby et al. 1997). The conversion of the free-flowing 

Columbia River to a series of reservoirs is another habitat change that has enhanced predation on 

salmonids by the northern pike minnow (Rieman et al. 1991). Shively et al. (1996) observed a rapid 

shift in the diet of the northern pike minnow from largely non-fish items to a diet composed mostly 

of juvenile salmonids following a release from Dworshak National Fish Hatchery. The shift was 

observed away from the release site in an area where the river changed from free-flowing to 

impounded. 

Any manipulation of hatchery practices to reduce predation will require better understanding of the 

ecology of the receiving waters than we have today. The size, time and place of release of hatchery 

fish might be altered to reduce predation on the wild salmonids or reduce predation on the artificially 

propagated salmonids. The importance of predator avoidance behavior has led to suggestions that 

salmonids undergo specific training to enhance their recognition of predators, improve their ability

to escape and increase their post-release survival (Maynard et al. 1995). Predator training in the 

hatchery is showing some promise in reducing predation on artificially propagated salmonids, but it 

is far from being universally implemented. Managers should also consider the indirect effects of 

habitat change in enhancing predation, especially if a hatchery is operating in the watershed. 

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4. Disease:

Definition -- Disease is the negative ecological interactions between a host, a pathogen, and the 

environment that results in an impairment that interferes with or modifies the performance of normal 

functions of the host. 

Theory -- The theoretical aspects of disease dissemination have been extensively studied in humans 

and some animal populations (see Anderson and May 1979, 1982; May and Anderson 1979; 

Grenfell and Dobson 1995). Theoretical treatment of disease processes in fish, however, have been 

only recently been explored for Atlantic herring, Clupea harengus (Patterson 1996); European 

flounder, Platichthys flesus (Lorenzenen et al. 1991); guppies, Poecilia reticulata (Scott and 

Anderson 1984), and domesticated trout (Bebak 1996). Reno (1998) has reviewed many of the 

critical factors involved in constructing models of disease dynamics for fish populations, but he did 

not specifically address transmission between hatchery and wild fishes. 

Evidence -- Diseases and their effects on fish populations result from multifactorial and interacting 

causes making cause-and-effect relationships difficult to determine (McVicar 1997). Detecting and 

verifying the transmission of disease between hatchery and wild fish is very difficult. Nevertheless, 

several examples illustrate the potential. Two examples come from Norway. In 1985, infected 

Atlantic salmon smolts transferred from Scotland introduced frunculosis into Norway. The disease 

has spread to 20 Norwegian rivers (McVicar 1995). In 1975, the parasite Gyrodactylus salaris from 

an infested hatchery in Sweden was introduced into the Lakselva River, Norway. Atlantic salmon 

parr, (Salmo salar), which were susceptible to the parasite, were heavily infected and within two 

years the abundance of parr had collapsed (Sattaur 1989). 

 

A recent example from the United States is the spread of salmonid whirling disease (Mysobolus 

cerebralis). The disease was first found in the United States in Pennsylvania in 1956. Since then it 

has gradually spread to a least 21 states. The likely cause of the spread of the parasite is the shipment 

of infected fish to new areas (Bergersen and Anderson 1997, Modin 1998). 

The introduction of new diseases to areas with no previous history of that pathogen is one way 

hatcheries can influence the mortality of wild fish. Another way is through the direct transmission of 

an endemic disease in a watershed from infected hatchery fish to the wild fish. This would be 

difficult to identify, and we could find no documented examples. 

84
Management agencies recognize the importance of this problem and have taken steps through the 

IHOT process to prevent the transfer of infected fish (IHOT 1994). The adequacy of the IHOT 

policies are discussed elsewhere in this report. 

5. Behavior: 

Hatcheries may alter the behavior of cultured fish as a consequence of domestication (genetic 

change) and as a consequence of acclimation to the hatchery environment without genetic change. 

Evidence for behavioral changes due to domestication is presented in the section on genetic impacts 

of artificial production. 

Differences in spawning behavior have been observed in comparative studies of wild coho salmon 

and coho salmon that were captured in a stream as emergent fry and reared in a hatchery 

environment until mature. Salmon reared in the hatchery from fry to maturity exhibited all the 

normal reproductive behaviors and they successfully spawned. However, when mixed with wild fish 

their reproductive success was reduced because of a diminished competitive ability (Berejikian et al. 

1997). Wild males dominated access to spawning females in 86 percent of the spawning events 

observed. Hatchery-reared females constructed fewer nests and started the typical spawning behavior 

later than wild females. Since these differences in behavior were observed after less than one 

generation in the hatchery, the observed effects were probably due to environmental effects on the 

phenotype (Berejikian et al. 1997). Fleming and Gross (1992 and 1993 cited in Jonsson 1997) 

observed similar results in their experiments with hatchery and wild coho salmon. Fifth-generation 

hatchery Atlantic salmon also showed less aggressive spawning behavior than wild fish (Jonsson 

1997). 

The obvious way to reduce the effect of the hatchery on spawning behavior is to minimize the 

differences in the hatchery and natural environments. However, which aspects of the hatchery 

environment need to be changed and how much change is needed is not known.

F. Populations and Production Trends Over Time 

As discussed elsewhere in this document, hatcheries were started in response to the decline of

returns from overfishing. Whether or not early hatchery production made any contribution, 

hatcheries were still viewed as the solution to mitigate for the anticipated loss in harvest resulting 

85
from river development. With successive construction of the dams beginning in the 1930s (Figure 

16), habitat was not only totally eliminated upstream from the barriers of Chief Joseph/Grand 

Coulee, Dworshak and Hells Canyon dams, but spawning and rearing habitat were also altered and 

lost below these dams as the result of the nearly continuous line of reservoirs that now represent the 

portions of the mainstem rivers “accessible” to anadromous salmonids. 

Figure 16. Dams on the Columbia and Snake rivers. 

In response to the anticipated reduction in natural production from loss of habitat, hatchery 

construction went forward with major facilities designed to replace the anticipated loss in harvest. 

Hatchery production responded with a consistent and growing contribution over the years (Figure 

17). Since 1950, the contribution from hatcheries increased from 38 million juveniles to 150 million 

by 1979, and has remained around 120 million since that time. 

86
Figure 17. Hatchery contribution to Columbia basin juvenile 

salmonid emigration. (Mahnken et al, 1997: Fish Passage 

 Center) 

In the meantime, the results of increased hatchery production were equivocal in terms of influencing 

the returning numbers of adult salmon and steelhead. Salmonid populations entering the Columbia 

River have shown a fluctuating range in escapement from 420,000 to 650,000 fish from counts over 

Bonneville Dam (Figure 18). The peak return in recent years was in 1987, following a weak but 

general trend with increased hatchery production. However, while hatchery production surged to an 

increase of over 100 percent from 1969 to 1980, returning adults are shown to have simultaneously 

decreased about 30 percent over the same time period. 

87
Figure 18. The trend in returning anadromous salmonid populations 

counted over Bonneville Dam on the Columbia River. (SteamNet 1996) 

The contrasting trends between artificial production and return over these years makes it uncertain 

what portion of the return can be attributed to hatchery production, and underscores the need to 

complete the intensive examination of hatchery performance. The loss of habitat from dam

construction reduced the natural production potential, which hatcheries were intended to replace. 

Total return of all anadromous salmonids, including commercial landings, has shown a relatively 

level trend to the 1990s, and a significant decline after that (Figure 19), while hatchery production 

remained the same. It should be noted, however, that salmon abundance already was depressed by 

the 1930s -- and hatcheries had been operating for 60 years. 

88
Figure 19. The trend in total production of returning 

anadromous salmonid populations to the Columbia River plus 

 commercial landings. (SteamNet 1996) 

In retrospect, the number of returning adult salmon was relatively level from 1938 through 1990. 

The precipitous loss of returning chinook entering the Snake River (Figure 20) accounts for a major 

share of the decline that has occurred in total return to the Columbia. 

A serious impact on the recent returns to the Columbia River Basin, therefore, appears to have been

from the construction of the four lower Snake River dams. Mitigation has not maintained adult 

returns to the Snake River at the level that existed prior to the construction of Ice Harbor Dam. 

However, there has been a high mortality of emigrating juveniles while making their migratory 

journeys through the altered mainstem corridor. The cumulative effects of the successive 

developments along the corridor impacted the hatchery fish as well as the wild fish, creating a more

complex problem as developments expanded than what was probably anticipated. If there is any 

hope of reaching the goal of replacement, survival through the lower Snake River will have to 

improve before the mitigation objective can be reached. 

The ascendancy of ecosystem management in the Columbia has further complicated the problem of 

addressing mitigation responsibilities on the river. Mitigation with hatchery production was not 

founded on the paradigm of ecosystem management, but simply one of replacing fish for fish in the 

harvest. Under the new concept, ecosystem health is a priority of equal importance as mitigation for 

lost harvest, which means the original process of satisfying mitigation will have to change. Hatchery 

success is no longer measured solely by the number of adults returning. Part of the problem in the 

decline of wild fish production is attributed to the impact of the very hatchery fish meant to mitigate 

89
for harvest reduction through overdrafts of wild fish in mixed stock fisheries. Hatchery fish can 

sustain higher harvest rates because of lower escapement needs (less than 10 percent) to supply 

production requirements. Wild fish, requiring higher escapements (30 percent to 60 percent) for 

adequate production, suffer the same rate of exploitation in mixed stock fisheries targeting hatchery 

fish. The cumulative effect, uncontrolled, is to drive natural populations down to eventual 

extinction. Prior to ecosystem management, and the pivotal importance of maintaining natural 

production in the basin, hatchery fish were viewed as a replacement option for wild fish, and could 

be used as the rationale for over-fishing wild fish in mixed stock fisheries. It was with the same

justification that hatchery fish could be viewed as mitigation for extirpating the runs above Grande 

Coulee and Hells Canyon dams. 

Figure 20. Chinook salmon returns to the Snake River related 

to the years when lower Snake dams were built. 

The ecological impact of hatchery fish is an issue of equal importance to mixed stock fisheries with 

regard to the long-term health of natural populations. Although there is little evidence to support 

some of the more theoretical concerns about hatchery fish altering the fitness of wild populations 

(Campton, 1998), the premise is not disputed, only the direction and degree to which such effects are 

manifest. 

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VIII. Conclusions and Guidelines

To briefly review, hatchery production of Columbia River Basin salmon started before the turn of 

the century for the purpose of augmenting harvest of chinook salmon for the commercial fishery. 

Science initially had only a small role in the process -- primarily the development of fish husbandry. 

Over time, the role of science evolved to include formal attention to nutrition, genetics and 

pathology. That attention, however, centered primarily on the technology of fish husbandry, with 

little attention to concerns about hatchery fish interaction with wild fish, or with the natural (postrelease) environment. 

With the new paradigm of ecosystem function, science articulated a refreshed interest in community 

balance, food chain dynamics, population structure, and integration of hatchery fish as a functional 

component of the ecosystem. Standard hatchery procedures no longer were accepted as a means of 

addressing augmentation or mitigation, and much greater emphasis is placed on developing a new 

conceptual foundation under which artificial propagation should proceed. The architects of this new 

conceptual foundation cannot be oblivious to the fact that the Columbia and Snake rivers are systems 

substantially altered from the historical conditions in which anadromous salmonids evolved. 

This report is not a commentary establishing the role of artificial production in future Columbia 

River fisheries management, or recommending the degree to which hatchery production should 

contribute in the basin. That is the responsibility of the state and tribal fisheries managers. This 

report concerns the state of the science that relates to artificial production, and in that regard presents 

guidelines that we believe should be the foundation of recommendations on the appropriate use of

artificial production in the future. Following the points of general agreement with the three recent

scientific reviews that broadly addressed hatchery operations (ISG, NRC, NFHRP), the guidelines 

are presented in two parts. First are guidelines based on our scientific assessment of artificial 

production that includes hatchery practices, ecological, and genetic considerations. Second are 

guidelines that address what we consider the necessary research to resolve problems and questions 

about the technology and management of hatchery programs. 

To provide further background for our guidelines, it is appropriate to discuss generally what is 

known and not known about hatchery effectiveness and hatchery effects. The level of knowledge 

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varies considerably for different aspects of the effects of hatchery management and policy. The three 

major divisions of this material are knowledge about: 

1. Effects of hatchery practices on the egg to smolt phase of the life cycle of hatchery fish; 

2. Effects of hatchery practices on the post-release phase of the life cycle of the hatchery product, 

and, 

3. Effects of the hatchery product on the wild stocks with which they interact ecologically and 

genetically. 

The amount and certainty of the knowledge in each of these three divisions is so different that we 

cannot reasonably attain the same level of conclusiveness about them from our review of the science. 

In order to attune our conclusions with the differing levels of certainty, we offer our advice in the 

form of recommendations, guidelines and hypotheses. And we urge our audience to be sensitive to 

the distinction and the implications of these guidelines, recommendations and hypotheses. 

Basically, the current state of the science can support firm “recommendations” about practices to 

enhance the performance of the hatchery product in the egg-to-smolt phase of the life cycle. The 

science is less comprehensive and conclusive about the post-release performance of the hatchery 

product. For this aspect we can offer tentative “guidelines” for practices that we are reasonably sure 

will generally improve post-release performance somewhat, but we can’t be sure how much, and we 

can’t offer assurances that these guidelines in themselves will be sufficient for meeting objectives of 

the program. The science is even less conclusive about the effects of the hatchery fish on wild 

stocks. The science can identify specific genetic and ecological mechanisms that must be operating 

in the interaction between hatchery and hatchery fish, but the degree of quantification and empirical 

verification in this important aspect of our knowledge is so low, that for the most part we can only 

state important, plausible “hypotheses.” The monitoring, analysis, and experimentation necessary to 

arrive at conclusions about these hypotheses should be elevated in priority for the future. In the 

meanwhile, we advise managers and policy makers to adopt a precautionary approach in the 

decisions where these hypotheses have a bearing. 

The picture is further complicated by the very real possibility of working at cross-purposes by 

simultaneously attempting to manage for improved egg-to-smolt performance within the hatchery, 

improved smolt-to-adult returns of hatchery fish, enhancement of wild stocks through 

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supplementation, preservation of wild stocks with captive breeding, and minimization of potential 

negative effects of augmentation hatchery operations on wild stocks. Practices that are good for one 

objective could be bad for another. A successful overall hatchery policy will have to be cognizant of 

these possible effects “between compartments.” We will discuss these trade-offs in the third, 

synthesis phase, of our review. 

A. Points of General Agreement with Recent Reviews 

The three recent independent reviews of fish and wildlife recovery efforts in the Columbia River 

Basin addressed hatcheries among other issues -- one report addressed hatcheries specifically. These 

reviews collectively represent a concerted effort to assess hatchery production from the scientific 

perspective. There was consensus among the three panels, which underscores the importance of their 

contributions in revising the scientific foundation for hatchery policy. The ten general conclusions 

made by the three panels are listed below. 

1. Hatcheries generally have failed to meet their objectives. 

2. Hatcheries have imparted adverse effects on natural populations. 

3. Managers have failed to evaluate hatchery programs. 

4. Rationale justifying hatchery production was based on untested assumptions. 

5. Supplementation should be linked with habitat improvements. 

6. Genetic considerations have to be included in hatchery programs. 

7. More research and experimental approaches are required. 

8. Stock transfers and introductions of non-native species should be discontinued. 

9. Artificial production should have a new role in fisheries management. 

10. Hatcheries should be used as temporary refuges, rather than for long-term production. 

Given the present degree of uncertainty about hatchery success, the SRT agrees that unified hatchery 

management policies should include plausible hypotheses that test some of the uncertainties inherent 

in these conclusions. 

In particular, with respect to the hypothesis that the future role of hatcheries in fisheries management 

will evolve considerably, we note that the priorities of fisheries management have changed 

significantly in recent years, so the needs that hatcheries should serve are also changing. The 

ongoing reality of increasing numbers of Endangered Species Act listings of anadromous and 

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resident fish puts a much higher emphasis on wild stocks and naturally spawning stocks. This 

increases the concern over the potential for artificial production to cause genetic and ecological harm

to such stocks. But it also raises the possibility that hatcheries may serve some positive role in this 

era of new priorities. 

B. General Considerations of the State of the Science and the Technology 

The goals sought by hatchery programs have changed over the years. However, like earlier hatchery 

programs, the most recent efforts of augmentation, supplementation and captive brood stock 

production may have succeeded in their numerical production objectives with regard to juvenile 

releases. The issue is that the effect of that production on increased return has generally not been 

demonstrated, and that effects on naturally spawning stocks have not been adequately 

investigated. Agencies have evaluated some hatchery procedures, such as the effect of size and time 

of release on return success, but there has been a general lack of effort at the programmatic level. 

Only recently has natural production in the Columbia basin been given priority. Previously, the 

approach of concentrating artificial production of Pacific salmon downstream from lower Columbia 

dams was considered a viable mitigation option for providing the necessary production from the 

system, based on general trends in hatchery production returns. However, if evaluations 

demonstrating the consistent production benefits of hatcheries have been undertaken, they have not 

been published in the peer-reviewed literature. Such publications are required to provide fair 

analysis of these hatchery programs. Issues of genetics, stock transfers and limiting effort to 

avoid overfishing wild stocks mixed with hatchery fish are symptomatic of the previous philosophy 

downplaying the role of natural production and the human alteration of the natural Columbia River 

Basin ecosystem. Given the present emphasis on the ecosystem approach, these issues are now 

important and should be given priority in the development of the new conceptual foundation for 

artificial production. 

In the past, weak native runs have been replaced with other fish in the development of hatchery 

programs, such as the original plan regarding Sooes River fall chinook salmon. Such action 

is inconsistent with present values. Diversity is now believed to be one of the keys to the long-term

success of salmonid populations, and adaptive traits should never be willfully abandoned. In 

situations where a stock has been extirpated, managers need to have the option of introducing nonnative fish to establish the nucleus on which restoration can take place. Even in this situation, 

however, the donor stock chosen should not be simply based on egg availability. Careful analysis is 

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required to assure environmental relationships between donor and target streams are as compatible 

as possible for the stock selected. Frequently, appropriate donor stocks will come from ecologically 

similar and geographically adjacent streams or watersheds. 

Stock transfers and introductions can place serious risk on native fish stocks and should be 

discontinued from hatchery programs except when the purpose is to restore an extirpated run or 

population. Introductions also might be justified when genetic diversity is so low as to threaten the 

persistence of a population. 

The primary role of hatcheries in the basin is mitigation for the loss of harvest as a result of 

reduction of habitat from economic development of the Columbia and Snake rivers. Given the 

present encroachment of habitat modification and degradation into the riparian and adjacent lands of 

these river systems, it is unlikely that natural production in a recovered ecosystem would 

satisfy commercial, tribal, and sports harvest interests. The options, therefore, are (1) to be content 

with lower production from managed natural populations and use hatcheries in a more temporary 

role for rehabilitation, or (2) to manage for greater harvest potential from a combination of natural 

production and hatcheries mitigating for habitat no longer accessible. Mitigation hatcheries are a 

long-term commitment involving significant cost. Although Columbia Basin hatcheries have not 

satisfied their objective of sustaining production thus far, nonetheless they now account for the 

majority of production in the basin. 

Changing the manner in which hatcheries address their role is the hope that hatcheries can succeed. 

Based on past hatchery performance in the basin, such expectation is bereft of proof. But abrogation 

of the concept based only on the past is also imprudent when hatchery management has made such 

serious mistakes and the fish still persist. As Reisenbichler (1998) reasoned after observing fish in 

the hatchery environment, ".. substantial adaptation to hatchery conditions [occurs]... and holds 

promise that modifying hatchery conditions can reduce deleterious genetic differences between 

hatchery and wild fish." The hope is that with care given to appropriate changes in the hatchery 

environment, the response of hatchery fish can be compatible and complementary to the natural 

population structure of the native species. The normative ecosystem is an equitable mix of natural 

and cultural features with environmental equity to sustain all life stages of a diverse mixture of 

healthy wild anadromous salmonids, concurrent with cultural and economic development of water 

resources. Hatcheries can have a mitigation role in the normative ecosystem. These may 

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become rehabilitation programs that secure the endurance of native runs. They may also become

perpetual programs to supply commercial or angling opportunities. The challenge is to redevelop the 

concept of a hatchery to assure enhanced production to meet both ecological and economic 

objectives. 

C. Relation to an Ecological Framework 

It is imperative that priority be given to the development of a set of scientific guidelines that serve as 

a conceptual foundation for the Columbia basin hatchery program. These also must be consistent 

with the eight elements of the basin-wide ecological framework (NPPC Document 98-6) that is to 

guide management of the Columbia River as an ecological system. The eight ecologically 

based elements are listed below. 

• The abundance and productivity of fish and wildlife reflect the conditions they experience in 

their ecosystem over the course of their life cycle. 

• Natural ecosystems are dynamic, evolutionary, and resilient. 

• Ecosystems are structured hierarchically. 

• Ecosystems are defined relative to specific communities of plant and animal species.

• Biological diversity accommodates environmental variation. 

• Ecosystem conditions develop primarily through natural processes. 

• Ecological management is adaptive and experimental. 

• Human actions can be key factors structuring ecosystems. 

The set of scientific principles that relate to artificial production, and emphasized by the latter two 

elements listed, are meant to minimize unintentional human influences on ecosystem structure. 

These principles can be divided along technological and managerial lines, differentiating between 

how hatchery fish are produced and how hatchery fish are used. 

D. Guidelines on Hatchery Practices, Ecological Integration and Genetics. 

Management of all hatcheries should be consistent with the life history of the cultured stock and the 

environmental conditions of the watershed, especially the annual temperature regime of the 

relevant section of native habitat represented in the stock of fish propagated. Life history strategies 

demonstrate the optimum course of action in the complexity of selective pressures exerted on 

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them (Brannon, in press). Proper management, therefore, must include only measures that are 

consistent with those life histories, or severe impacts on the native populations should be expected. 

Management policy on such conventions as stock introductions (listed above), size and time of 

release, magnitude of release, genetic agenda, and recovery strategies are of major importance to the 

success of hatchery programs. Details on these issues are in the following guidelines, but it needs to 

be understood that in many cases where scientific principles are advocated, applied evidence is 

not available to demonstrate the precept. In these cases, it may be more appropriate to view the 

guidelines as hypotheses that need to address problems they exemplify -- as safeguards 

against unforeseen events that could destroy the viability of the runs managers are attempting to 

conserve. Some theories are troublesome to practitioners because their experiences do not support 

the axiom. Concerns about inbreeding are an example. Many populations of salmonids are small and 

inbred by the nature of the environment describing their habitat. In fact, where certain traits are 

critical to their survival, such as an innate complex orientation pattern to reach a destination, 

specificity rather than diversity defines fitness. This appears contrary to the theory, but in the 

broader range of the species, diversity is still the key to species stability. Measures taken to maintain 

the diversity present, or to prevent potentially negative effects of induced inbreeding, even within 

naturally inbred lines, are precautions that safeguard against artificially imposing a deleterious 

artifact of hatchery production on a population. 

Present technology is bringing into application measures that improve the quality of fry at the time 

of emergence and at readiness of juveniles to enter the migratory phase. Providing 

required nutritional needs in a form available in artificial diets were some of the first advancements 

in hatchery technology (Hublou, 1963), and nutritional develops have continued (Forster and Hardy, 

1995). 

Substrate and darkness during incubation to maximize energy efficiency for growth are now 

employed routinely. These conditions were found to more accurately simulate natural 

incubation environments and produce larger fry at emergence than open tray or basket incubators 

(Brannon, 1965). Other technologies are also being employed, and their appearance in the list only 

reaffirms the importance placed on them. 

Guideline 1. Technology should be developed and used to more closely resemble natural 

incubation and rearing conditions in salmonid hatchery propagation. 

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In developing hatchery technology, hatchery programs should work toward the goal of providing 

environments that resemble natural conditions during artificial propagation. These may include: 

• Incubation in substrate and darkness; 

• Incubation at lower densities; 

• Rearing at lower densities; 

• Rearing with shade cover available; 

• Exposure to in-pond, natural-like habitat; 

• Rearing in variable, higher velocity habitat; 

• Non-demand food distribution during rearing; 

• Exposure to predator training; 

• Minimize fish-human interaction;

• Acclimation ponds at release sites; 

• Volitional emigration from release sites. 

Rationale: Lower rearing densities, minimum exposure to humans, and shade cover over raceways 

enhances fish quality and maintains a behavior more similar to that of wild fish. Also, volitional 

migration when the fish are ready to begin their journey to sea is a technology practiced at some

hatcheries, promoting natural transit behavior and less impact on the carrying capacity of the 

receiving stream or other water body. These are positive advancements in hatchery production 

operations that are encouraged to continue. Other practices need research on potential indirect 

effects. For example, although accelerated rearing can easily overcome any size deficiency of the 

fry experienced at the time of emergence, what isn't known are the potential impacts accelerated 

rearing will have on the normal biological development from embryo to fingerling, or the impact that 

large hatchery fish have on their wild counterparts. 

Guideline 2. Hatchery facilities need to be designed and engineered to represent natural 

incubation and rearing habitat, simulating incubation and rearing experiences complementary 

with expectations of wild fish in natural habitat. 

Rationale: Hatchery technology in the Columbia basin has relied primarily on standard tray 

incubation and concrete raceway technology based on engineering designs that emphasize efficiency 

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and convenience for fish culture operations. Qualities associated with natural habitat have not been 

incorporated in such designs, and fish reared in standard concrete raceways learn behavior conducive 

to those situations, and out of harmony with what they will experience when released into natural 

conditions. Comparatively poor survival success of hatchery fish is attributed in part to such 

experiences atypical of natural conditions. Technology needs to design facilities that utilize 

engineered earthen stream channels that represent natural habitat with cover, glides and pools, 

woody debris and flow patterns mimicking natural habitat. Incubation and rearing could take place 

in the same channel facility, at densities appropriate to encourage natural feed (supplemented with 

formulated diets) and provide learning opportunities under simulated natural conditions. Training 

would include exposure to size variability among other species that share the habitat, and limited 

exposure to predation. 

Guideline 3. New hatchery technology for improving fish quality and performance needs to 

have a plan for implementation and review at all hatchery sites, where appropriate, to assure 

its application.

Rationale: Assuring that technological advances in hatchery propagation are part of 

hatchery operational plans is critical to the implementation of changes meant to improve the quality 

and performance of hatchery fish in the natural environment. Often such implementation occurs only 

among those hatcheries where a willingness to make changes exists, given that information on new 

technology is even transmitted. It is important that technological advancements are first verified and 

the mechanism through which such technology enhances quality or performance is well understood. 

Then there needs to be a process for implementing the technology, with accountability for its 

installation and review to make it as routine as feed delivery, assuring its application and evaluation. 

Guideline 4. To mimic natural populations, anadromous hatchery production strategy should 

target natural population parameters in size and timing among emigrating anadromous 

juveniles to synchronize with environmental selective forces shaping natural population 

structure. 

Rationale: Hatchery programs have tended to concentrate on large-size fish at the time of release, 

as well as varying the timing of release, to facilitate higher return success. Although such rationale is 

understandable from the standpoint of improving hatchery fish survival, such practices introduce 

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atypical migrants that create an alteration in the natural continuity of events around which population 

strategies have evolved. With the exception of fall chinook that normally show variation 

in migratory distribution patterns, such practices with other anadromous salmonids are believed to 

have negative effects on fitness of wild fish, and may perturb population structure to the 

disadvantage of natural populations. Based on interpretations of population structure and life history 

patterns (Brannon, in press), avoiding atypical size and time at migration among hatchery fish is 

desirable, even with the immediate disadvantage it may have on hatchery return success. The point is 

that hatcheries should focus on mimicking the natural environmental selective forces within the 

target watershed so hatchery-produced emigrating juveniles exhibit the same size distributions as 

juveniles from the natural population. 

Guideline 5. To mimic natural populations, resident hatchery production strategy should 

target population parameters in size and release timing of hatchery-produced resident 

juveniles to correspond with adequate food availability and favorable prey to maximize their 

post-stocking growth and survival. 

Rationale: Post-stocking mortality of a wide array of resident fish species could be reduced by 

implementing release strategies that match released fry or fingerlings with periods of adequate 

production and availability of planktonic and invertebrate food items. Attention to vulnerability 

of stocked resident fish fry or fingerlings as prey, and abundance and behaviors of potential 

predators in receiving waters can also significantly improve initial post-stocking survival. 

Guideline 6. Supplementation hatchery policy should utilize ambient natal stream habitat 

temperatures to reinforce genetic compatibility with local environments and provide the 

linkage between stock and habitat that is responsible for population structure of stocks from

which hatchery fish are generated. 

Rationale: Temperature is a crucial factor affecting adult salmonid return timing and spawning 

(Brannon, 1987), and is an important factor affecting the length of time juveniles spend in stream

residence before migrating to sea. This fundamental influence has formed the framework around the 

evolution of salmonid population structure. Temperature demonstrates its pivotal effect on 

the evolution of life history forms through temporal influences on egg incubation and juvenile 

growth as the basis for differentiation of adult timing and juvenile residence behavior, respectively. 

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It is argued, therefore, that temperature is one of the most critical environmental factors affecting life 

history forms peculiar to their respective stream system. Temperature is the environmental 

parameter motivating the evolution of stock predispositions selectively reinforced over time to 

represent genetically distinct units. Temperature regimes during early life history are typically 

altered from the natural pattern by hatchery use of ground water for incubation. Hatchery 

management policy should adhere to using the ambient temperature regime of their natal 

environments to maintain the compatibility of hatchery fish with the natural system and 

the effectiveness of hatchery contribution to the natural spawning population. In some cases, wild 

fish spawn on spring-fed reaches of streams, and the appropriate incubation temperatures in 

those situations would be incubation substrate temperatures. However, when it comes to the rearing 

phase where the growth rate is determined by temperature (Brett et al, 1969), it is the daily ambient 

mean temperature that is important to follow. 

Guideline 7. Salmonid hatchery incubation and rearing experiences should use the natal 

stream water source whenever possible to enhance homestream recognition. 

Rationale: Another factor associated with the natal habitat and homing accuracy is the homestream 

odor profile that provides the fingerprint ultimately identified with the homestream spawning 

and incubation site. Hatchery programs not only use ground water for incubation, but hatcheries are 

usually away from the natal environment to which local stocks have adapted. The assumption is that 

by planting the fish in the proper location, hatchery fish will home to that stream on return. While 

this is true, imprinting is sequential (Brannon and Quinn 1990; Quinn et al. 1990), and 

the incubation environment is the first odor cue on which alevins imprint and the ultimate identity 

sought by returning fish (Brannon 1982). Strays are common in some hatchery populations and lack 

of having imprinted during the incubation phase is suggested as being responsible for higher stray 

rates. To assure the continuity between hatchery fish genetics and local stream habitat, the water 

sources closely linked with the natal environment are most desirable. This guideline is most difficult 

to incorporate with present hatcheries because the capital structure and water system have been 

established without those priorities. New facilities, however, should be located on sites with access 

to appropriate water sources. 

Guideline 8. Hatchery release strategies need to follow standards that 

accommodate reasonable numerical limits determined by the carrying capacity of the 

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receiving stream to accommodate residence needs of non-migrating members of the release 

population. 

Rationale: Standards should include impact considerations on the wild fish residing in the system, 

and should be based on life history requirements of the cultured stock. Hatchery releases of cultured 

fish into receiving streams occur under the assumption that the river is used primarily as a migratory 

conduit to the estuary. This is true for only those fish (smolts) at emigration readiness. Fish not ready 

to migrate will take up transitional residence in the stream, causing the potential negative 

interactions with wild fish present. Care should be taken to limit release numbers consistent with the 

estimated rearing capacity of the system to minimize impacts on wild fish. Moreover, the practice of 

releasing fish to make space for other broods should be discontinued. Release of hatchery fish must 

fit a schedule consistent with life history requirements of the natural population from which the 

brood lot was derived. 

Guideline 9. Hatchery programs should dedicate significant effort in developing small 

facilitates designed for specific stream sites where supplementation and enhancement 

objectives are sought, using local stocks and ambient water in the facilities designed around 

engineered habitat to simulate the natural stream, whenever possible. 

Rationale: Hatcheries are most often developed around the concept of a central facility from which 

fish are outplanted to many other streams or acclimation ponds, not always using native stocks in 

each instance. The rationale is usually related to the major capital expenditures for hatcheries under 

the old hatchery concept. It is much more desirable to locate smaller, stream-specific operations to 

maintain stock identity with the particular stream targeted. Nothing larger than a station capacity of 

100,000 eggs or 25,000 fingerlings would be required on smaller tributary systems. This would 

require no more than a rearing channel to accommodate such small inventories, but small numbers 

in natural-like habitat is the ideal for supplementation of native salmonids. Even fry releases can be a 

feasible option to consider under these circumstances associated with the natural habitat, 

when conditions for supplementation can call for such limited, and perhaps temporary, artificial 

application. Again, this hypothesis is impossible with present facilities located where they are and 

with capital commitments in water and concrete. However, with new artificial production facilities, 

part-time stations of this nature would address both the biological and ecological requirements 

that future operations must satisfy. 

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Guideline 10. Genetic and breeding protocols consistent with local stock structure need to be

developed and faithfully adhered to as a mechanism to minimize potential negative hatchery

effects on wild populations and to maximize the positive benefits that hatcheries can contribute 

to the recovery and maintenance of salmonids in the Columbia ecosystem.

Rationale: As an integral component in a complex ecological system, salmonid stocks have 

evolved with their environments. Spawning time, emergence timing, juvenile distribution, marine 

orientation and distribution are not random, but rather occur in specific patterns of time and space 

for each population (Brannon 1984), and include behavior that evolved under historical abundance 

constraints in natural populations. The appropriate seed stock is key to producing viable, healthy fish 

for the respective system. Given the ecosystem concept for management protocol in the Columbia 

Basin, population genetics and the natural environment salmonid stocks have evolved under have to 

become blueprints in hatchery programming. Differences between the genetics of wild stocks and 

hatchery fish (Ryman and Sthl, 1980; Allendorf and Utter, 1979) are considered by the SRT as a 

major source of poor hatchery fish performance in the wild. Development and adherence to strict 

genetic guidelines and breeding protocols consistent with local population structure is essential for 

effective hatchery contribution to wild production and maintenance of local genetic diversity. 

Guideline 11. Hatchery propagation should use large breeding populations to minimize

inbreeding effects and maintain what genetic diversity is present within the population. 

Rationale: One of the potential negative effects of artificial production is that relatively small 

breeding populations are involved in hatchery programs. Even when 100,000 fingerlings are 

scheduled for supplementation, that number represents a little over 25 females for brood stock, and a 

relatively limited representation of the gene pool. In the Idaho captive rearing project where 

juveniles are intercepted and reared to maturity as a means to avoid demographic risks of cohort 

extinction, only enough parr are captured to provide 20 spawners for each population, which is even 

a smaller representation of the gene pool. The risks in using small breeding populations are loss of 

diversity and magnifying the effect of deleterious genes. Hatchery survival can increase the 

contribution of the artificially propagated fish out of proportion with number, with the result that 

over time the hatchery population will become increasingly more represented among the natural 

spawners. The issue is not just inbreeding, because many healthy natural populations are very site103
specific in unique environments and represent inbred lines. The risk is that hatchery production can 

accelerate the potential harmful effects of inbreeding by involving only a small portion of the 

returning adults in the artificial breeding population. To avoid these negative effects of hatchery 

production, a large number of spawners should be included in the breeding protocol. When the run is 

relatively small, this may require live spawning, and removing only a portion of the eggs from each 

female and subsequently releasing the fish to continue spawning naturally. 

Guideline 12. Hatchery supplementation programs should avoid using strays in breeding 

operations with returning fish. 

Rationale: In situations where strays constitute a substantial proportion of hatchery return 

populations, care should be taken to avoid inter-stock hybridization because of the loss of adaptive 

traits in the resulting progeny. Reisenbichler (1998) demonstrated examples of reduced fitness from 

hybridization. Stock hybridization breaks down genetic homeostasis and disrupts co-adaptive gene 

complexes, which lowers the fitness of the local stock. A policy needs to be developed to minimize 

the contribution of strays to the local hatchery stock. In the situation where a hatchery is 

supplementing a native population, inter-stock hybridization should be avoided to prevent loss of 

adaptive fitness. 

Guideline 13. Restoration of extirpated populations should follow genetic guidelines to 

maximize the potential for re-establishing self-sustaining populations. Once initiated, 

subsequent effort must concentrate on allowing selection to work by 

discontinuing introductions. 

Rationale: When undertaking restoration projects where populations have been extirpated, 

restoration strategies need to be given careful consideration and reference to genetic guidelines. 

Where neighboring populations represent appropriate characteristics, stock transfer may be the best 

strategy. When suitable stocks are not available, or when information is insufficient with which to 

match a donor stock, then inter-stock hybridization may be an alternative. Inter-stock hybridization 

breaks down co-adapted gene complexes and releases genetic variability on which selection can 

work. Restoration can use different genetic-based approaches, depending on the situation, but the 

characteristics of the donor stock(s) are critical. The key is to follow through with the strategy 

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selected and allow sufficient time for the founders to be selectively established by avoiding 

continued introductions in the target stream. 

Guideline 14. Germ plasm repositories should be developed to preserve genetic diversity for 

application in future recovery and restoration projects in the basin, and to maintain a gene 

bank to reinforce diversity among small inbred natural populations. 

Rationale: One of the most important considerations in the Columbia Basin fisheries management 

plan is to preserve the existing genetic diversity. Diversity is inherent to the stability of the species. 

The various systems, with their component population networks, are the sanctuaries of variability.

Recovery and enhancement of natural production in the basin will not be a rapid process, and in the 

meantime further loss of diversity may occur, with some populations becoming extinct. It is critical, 

therefore, to launch an immediate program to preserve germ plasm by collecting and cryopreserving 

milt from all naturally spawning populations that can be reached. The technology is available and 

currently is being employed with some ESA-listed salmonid stocks. This effort needs to be expanded 

and given greater priority. Germ plasm should be collected from each population on more than one 

broodyear to develop as complete a repository as possible. The availability of germ plasm for future 

use in maintenance of diversity or restoration of extirpated runs will be invaluable in the long-term 

ecological framework of the managed river. 

Guideline 15. The physical and genetic status of all natural populations of anadromous and 

resident fishes need to be understood and routinely reviewed as the basis of management 

planning for artificial production.

Rationale: Knowing the status of the endemic stock where hatchery fish are involved is imperative 

under the ecological framework of fisheries management. Information should include life history, 

population structure and the habitat utilized. This knowledge must include, in addition to the 

traditional numerical status of the run, details on its population structure, distribution patterns, size 

and timing of migration, and the level of genetic specificity and diversity within the population. The 

habitat status associated with the population must also be known, including the area available, 

the condition of the habitat, new areas that can be developed, and the carrying capacity. This 

information is essential to the management of all native anadromous and resident species in the 

Basin, which will require ecological expertise at the programmatic and hatchery levels. 

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E. Guidelines on Research and Monitoring

Good management is the key to successful integration of hatcheries into a functioning and dynamic 

ecosystem. Research to improve artificial production, the extent of its application, and its limitations 

is basic to the effective management of hatcheries in the basin. In this regard, monitoring is also a 

critical element in the management process. Knowing what is successful and what must change 

is impossible without appropriate monitoring programs. 

Guideline 16. An in-hatchery fish monitoring program needs to be developed on performance 

of juveniles under culture, including genetic assessment to ascertain if breeding protocol is 

maintaining wild stock genotypic characteristics. 

Rationale: The NPPC needs to design a scientifically valid monitoring program for the basin 

hatcheries. Special attention should be paid to the collection of valid data that applies to 

routine assessment of juvenile performance in the hatchery incubation and rearing phase, up to the 

point of release. Genetic monitoring of the stock inventory would include descriptive evaluation at 

first feeding and at release time to assess if hatchery propagation is altering genotypes from that of 

the wild population. 

Guideline 17. A hatchery fish monitoring program needs to be developed on performance 

from release to return, including information on survival success, interception distribution, 

behavior, and genotypic changes experienced from selection between release and return. 

Rationale: The NPPC needs to design a scientifically valid monitoring program for hatchery 

fish performance after release from the culture facilities. In addition to return success, attention 

should be paid to relative interception distribution (tag analysis) of hatchery fish to compare 

performance parameters with native fish. Special attention should also be given to descriptive 

genetic assessment at time of return to determine if genotypes surviving are representative of 

genotypes released, and compatible with the native stock. With the advent of the PIT tag system, 

opportunities to gather more specific information exists. Significant insights can be gained on 

straying, migratory route and timing that are key to honing hatchery programs. 

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Guideline 18. A study is required to determine cost of monitoring hatchery performance and 

sources of funding. 

Rationale: A study should be undertaken to consider how much monitoring programs will cost and 

what reallocation of effort in the production programs would be required to fund adequate 

monitoring efforts where additional funds cannot be secured. 

Guideline 19. Regular performance audits of artificial production objectives should be 

undertaken, and where they are not successful, research should be initiated to resolve the 

problem. 

Rationale: Routine audits of hatchery production objectives should be established (for example, 

every five years) to determine if they are achieving their objectives. In those cases where programs

or hatcheries are not showing any production benefit, they should be re-prioritized to research-only 

until the problems can be resolved. In some cases, research may disclose that the objectives are not 

attainable. In those situations, emphasis can then be redirected, programs changed, or discontinued. 

Guideline 20. The NPPC should appoint an independent peer review panel to develop 

a basinwide artificial production program plan to meet the ecological framework goals for 

hatchery management of anadromous and resident species. 

Rationale: With the development of the broad ecological framework in the basin placing emphasis 

on hatchery management in the arena of conservation fisheries and ecosystem function, it will be 

necessary for practitioners and fisheries scientists to work together in developing the appropriate 

hatchery program plans to achieve the ecosystem goal. Problems that have prevented hatcheries 

from achieving their goals, or insights on what may be impossible to achieve in the ecosystem

approach at the hatchery level, cannot be ascertained without major contribution from hatchery 

managers experienced in the system. Also, the inherent conflict between the concept of ecosystem

management and the concept of management for harvest mitigation has to be resolved within the 

ecosystem framework. Those resolutions, and the development of the hatchery program 

plan addressing specific actions needed to achieve the goal, are essential elements early in the 

planning process. The responsibility will require appointment of an independent peer review panel 

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that can give careful and appropriate consideration, through solicitation of agency, tribal and public 

interests, to past management experiences. 

Given the new management emphasis on wild stocks, special consideration must be given to the 

possibility that some of the maladaptive traits developed by hatchery fish in hatcheries could 

be expressed even more deleteriously when those fish attempt to spawn naturally (in a 

supplementation program) or when they interact genetically (as strays) with natural spawning 

populations, or as they interact with natural stocks ecologically throughout the post-release portion 

of the life cycle. While these possible risks are in some sense the most alarming, they are also the 

most poorly documented, and the quantitative strength of the underlying forces are not 

well understood. Therefore, a large research and monitoring effort needs to be directed at these 

questions of genetic and ecological effects of hatchery fish on naturally spawning stocks. The results 

of these studies are needed to lay to rest some of the fears about worst-case scenarios, and they are 

also needed to teach us how to modify hatchery management to achieve the most positive kinds 

of interactions with wild stocks. 

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LITERATURE CITED

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APPENDIX

Regional scientific questions on artificial production addressed in this report: 

1. What are the ecological impacts of artificial production in the Columbia River Basin?

General o What are the positive biological/ecological contributions of artificial production in the

Columbia River?

o What are the negative biological/ecological impacts of artificial production in the 

Columbia River?

o Does it not make sense to alter stock composition in hatcheries based on ocean 

conditions?

Fitness o Can hatcheries be used to rebuild wild, native salmonid populations and maintain 

their genetic and life history attributes, their fitness and the evolutionary capacity of 

the populations?

o Are hatchery salmonids less fit for survival in the natural freshwater and ocean 

environments? If they are, what are the changes that must be made in the hatchery 

operation to make hatchery fish as fit as wild fish? 

o Is there a differential survival between hatchery and wild salmonids throughout their 

life cycle stages? Is there a differential survival rate for hatchery and wild fish as 

they encounter the human changes in the system? For example, do wild and hatchery 

fish survive dam passage, barging and predation at different rates? If they do, then 

should the agencies and tribes in their management programs acknowledge this 

differential survival rate? 

o Where have hatchery stocks caused the decline or extinction of wild stocks? Where 

have hatcheries enhanced the restoration of a wild stock?

o Can the biological diversity, fitness and productivity of a wild, native salmonid 

population be maintained with a hatchery?

o Do hatchery programs exist in the Columbia Basin or the region that have been 

shown to do a good job supporting biological diversity, genetic and life history 

attributes, fitness and productivity of the native population they interact with? Can 

they serve as a model for the basin and region?

o Should a coordinated gene flow management policy be developed to control stray 

hatchery fish in the basin?

Disease o Are hatchery disease treatment programs likely to create resistant pathogens that 

could pose a health risk to wild salmonids? What should be done to eliminate or 

manage this risk?

2. What is scientific context for the use of artificial production in the Columbia Basin? 

o What are the major research questions associated with artificial production?

o How does the existing level of scientific uncertainty affect the use and management 

of artificial production? 

o What are the priority research questions that need to be answered to integrate 

hatchery and wild production so that there is no loss of fitness and productivity in 

either the hatchery or wild populations?

o What is the historic relationship between natural production and harvest? 

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3. How has artificial production performed relative to its management goals? 

General o How effective has artificial production been relative to stated objectives in the 

Columbia River?

Harvest o How does artificial production affect harvest regimes and vice versa? What has been 

the affect of this relationship on natural production?

o How do we mitigate fisheries with the least impact on wild fish? 

o As the proportion of hatchery fish increases and harvests are targeted on them, a 

mixed stock harvest problem is created where the wild, native population is exposed 

to high harvest rates. In this way the hatchery program fuels the harvest management 

program and wild fish are overharvested. What are your recommendations for 

reducing or terminating this problem? Can hatchery fish be used as a buffer to 

protect wild fish or is this a rationalization to justify not making changes in fishery 

management?

o If harvest rates are constrained by natural production, then how can we alter 

hatcheries to meet compensation goals?

Mitigation o Can hatcheries be used to double the runs and, at the same time, maintain the 

biological diversity, fitness and productivity of the individual subbasin populations? 

Or is there a conflict between these two goals set forth by the fish agencies and tribes 

through the Power Planning Council? What are your recommendations for resolving 

this conflict, if it exists? 

o Mitigation has been carried out in such a way that the effect is the replacement of

wild, native salmonids with hatchery fish. Is this effective mitigation? Have the 

mitigation agreements and goals been met in each relevant case in the Columbia? If

hatchery mitigation is not working, what should it be replaced with that would protect 

wild populations?

o Given that hatcheries are a necessary tool to mitigate for lost natural production, 

where does is make most sense, (i.e. most effective in production and cost) to locate 

production facilities?

o Have mitigation hatcheries been successful in replacing numerical losses in the basin? 

Have they been successful in replacing the biological diversity and fitness of the wild, 

native runs that were lost?

4. What is the scientific basis for the use of supplementation? 

o What is the potential, and what are the associated risks, for artificial production to 

augment or supplement natural production in a biologically sound and sustainable 

manner?

o What are the hatchery protocols needed to prevent a hatchery population from

diverging from the wild donor population?

o Can it be assumed that a hatchery population derived from a wild donor population 

will not diverge from the donor population in genetic, life history traits, and fitness?

o How should a hatchery program be operated when reintroducing a salmonid 

population into a stream where the species has gone extinct if the goal is to promote a 

healthy, self-reproducing new population?

o Does hatchery supplementation of wild salmonids work? Is there evidence in the 

scientific literature that shows hatchery supplementation is able to maintain the 

biological diversity, abundance, distribution, productivity and fitness of the original 

wild, native population? If not, should the region continue to fund new hatchery 

supplementation projects?

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o Can these wild native populations be recovered using supplementation where wild 

brood stocks are used in the hatchery program?

o Can hatchery supplementation increase the numbers of fish while maintaining the 

productivity (fitness) of the affected population over time?

o Should hatchery and wild salmonids be integrated so that they function as single 

reproductive unit within a subbasin? Or should the two be kept separate, including 

the separation of spawning time to reduce crossbreeding between hatchery and wild 

fish?

5. What is the application to resident fish? 

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