McKenzie River Chinook Salmon: A Legacy Population in Peril

Spring Chinook Salmon spawning on the McKenzie River Photo: Arlen Thomason

By: Dave Thomas and Arlen Thomason, Reposted from The Osprey Issue No. 81

David Thomas is a member of the McKenzie Flyfishers and for 60 years a committed fly fisher, conservationist and nature photographer. Trained as a population biologist and biostatistician, he taught at the University of California and later was a researcher at NIH and in the pharmaceutical industry.

Arlen Thomason is Conservation Chair for the McKenzie Flyfishers, and is an author, outdoor photographer, and life-long fisherman. He trained as a molecular biologist and worked for many years in biomedical research. You can learn more about the McKenzie Flyfishers at:

The Willamette River originates in the Cascade Mountains and drains most of northwest Oregon, joining the Columbia River near Portland. The tributary rivers of the Upper Willamette River Basin (UWB) have supported a spring run of Chinook salmon (O.tshawytscha) since long before humans arrived. The stock is assumed to have evolved its early seasonal run timing in response to the need to pass the Willamette Falls near Oregon City when there was sufficient flow. It has been estimated that in the Nineteenth Century, Chinook escapement in the basin could have numbered 275,000, with approximately 40% returning to spawn in the McKenzie River subbasin. Since then, the wild Chinook population has decreased dramatically, with only two of seven subbasin populations still considered viable. Of those two, the McKenzie River population is by far the strongest, remaining the best hope for recovery of UWB Chinook salmon, and it has been designated a “legacy” or “stronghold” population by fishery managers. That fact notwithstanding, the McKenzie Chinook population has itself shrunk to an alarmingly small size, recently recording an all-time low. The “last best hope” for saving UWB Chinook salmon from complete extinction is in serious danger. How we got to this point and what is being done or could be done to reverse this trend is the subject of the remainder of this article. The usual suspects—habitat, harvest, hatcheries, and hydropower—all play their roles.

The McKenzie River begins high in the extensive lava field aquifer of the central Oregon Cascades and tumbles west for 90 miles through a National Wild and Scenic River corridor to its confluence with the Willamette River near Springfield. The river drains a basin of 1,340 square miles and is fed by several major tributaries, most notably the South Fork, which is 30 miles long and historically provided prime spawning habitat. Like the rest of the basin, the McKenzie subbasin saw substantial anthropogenic environmental (habitat) degradation during the late Nineteenth and early Twentieth centuries. By the late 1940s, an estimated 46,000 spring Chinook returned to the McKenzie River. Part of this reduction was certainly due to habitat degradation and water removal, particularly in the developed lower river. And though there is little or no exact documentation of the ocean and freshwater harvest in the lower Columbia River during the early years, it’s known that those rates were often extremely high, requiring strict regulations to avoid extirpation of the entire Columbia River salmon run.

Nevertheless, at that time it was proposed that the McKenzie River could potentially still support up to 80,000 spawning Chinook. However, between 1942 and 1969, a series of dams were constructed in the Willamette Basin, creating barriers to substantial proportions of spawning habitat. Three dams were constructed on the McKenzie River — Blue River Dam, Cougar Dam and Trail Bridge Dam —resulting in the loss of approximately 22% of potential spawning habitat.

Along with the wild population of McKenzie Chinook salmon, the Oregon Department of Fish and Wildlife (ODFW) or its precursors have maintained a hatchery stocking program on the river since 1907. Prior to World War II the Chinook hatchery program followed a practice of blocking the entire salmon run in the lower river to allow the collection of eggs and milt. Today this practice would be considered astounding; however at the time, fishery managers assumed that all fish of one species were essentially interchangeable and could be replaced or reassigned as Man found it convenient. At the same time, hatcheries were considered more efficient at producing fish equivalent to those spawned in nature. Thus it was thought that hatchery spawning was a boon both to the fish and to those who benefited from their harvest. Today we know differently about the true effects of hatcheries, a subject we will come back to below.

From 1945 to 1960 an average of 18,000 returning Chinook on the McKenzie River was observed, with a high of about 46,000. However the condition of the river changed substantially with the initiation of the Upper Willamette Project managed by the Army Corps of Engineers (COE). This project was intended to provide flood control, irrigation support, hydropower, and recreation opportunities in the Willamette Basin. The project ultimately resulted in the construction of 13 dams, starting in 1942 and completed in 1969. In the McKenzie River two dams, Blue River Dam on Blue River (1969) and Cougar Dam on the South Fork McKenzie (1963), were constructed. In addition, Trail Bridge Dam (1963) blocked the mainstem of the river for fish passage at river mile 82. The latter dam was constructed by a local utility company and is intended to provide power to the metropolitan area downstream. The same utility also owns Leaburg Dam on the McKenzie River, three miles east of the town of Leaburg. It was built in 1929 to divert water from the river’s mainstem to a hydropower plant. The water is subsequently returned to the river downstream. As the dam is of low height and has a functioning fish ladder it is not considered a serious impediment to fish passage. In total, these dams denied fish passage to about 40 miles of potential Chinook spawning habitat.

After dam construction was completed the number of naturally spawning Chinook in the McKenzie River continued to decline from the post-WW II baseline. The estimate for 1990-2005 was an average 2,104 wild Chinook returning annually. Most of the blame for the continuing decline has focused on the dams. However, while there is little doubt that the dams have contributed,they block access to only about 20% of the potential spawning habitat in the McKenzie basin, failing to completely explain the approximately eight-fold decline in the wild salmon population. Still, as dams were the most visible change and very likely had some impact, they seem to have become the preferred culprit. As a result, the COE and the State of Oregon agreed that as mitigation, the federal government would support McKenzie Hatchery production of about 840,000 smolts, based on the number of returning salmon that the dammed rivers were assumed to have otherwise contributed. The COE maintains ownership of the hatchery, which is managed under contract by ODFW. The number of Chinook smolts released in the McKenzie River from this hatchery averaged about 1,200,000 annually from 1990 to 2011, with ODFW funding production of the excess over 840,000.

Despite the concept that hatchery output was intended to “supplement” the native spawning Chinook numbers in addition to mitigating lost angling opportunity, there has been little or no evidence of a positive effect on wild Chinook salmon recovery. On the contrary, the fishery science literature has increasingly demonstrated that in most instances interaction between hatchery-origin and naturally-spawned anadromous fish exert strong negative effects upon the wild fish population. As the evidence has accumulated, attention of the scientific and conservation communities has progressively turned to the likelihood that hatchery operations are a major contributor to the demise of wild populations. (Araki and Schmidt 2010) Such harmful effects were already well known by 1999. In that year, as the number of McKenzie Chinook dropped below 1,500 spawners, the National Oceanic and Atmospheric Administration (NOAA) listed the spring Chinook salmon in the entire Upper Willamette Basin as threatened under the Endangered Species Act (ESA) and designated the spring Chinook salmon an Evolutionarily Significant Unit (ESU) of their species. Following listing, the agencies (in this case the COE, Bonneville Power Authority (BPA) and Department of Reclamation) responsible for managing the species were required to provide a Biological Assessment (BA) of the status of the species, factors contributing to its being threatened, and corrective actions that will lead to the species’ recovery. This document was prepared and sent to the section of NOAA that oversees these issues, the National Marine Fisheries Service (NMFS), which has the authority to approve programs or require changes it judges as “prudent and necessary” to improve the situation. Beyond the BA, a hatchery program that could harm the listed ESU requires submission and approval of a Hatchery Genetic Management Plan (HGMP) that defines the boundaries of the program, and describes actions that will be taken to assure that there are no effects that are significantly detrimental to recovery of the wild stock. Further, NMFS regulations require systematic monitoring of the status of the listed species or stocks so that trends, positive or negative, can be identified and the consequences of actions determined. Thus COE submitted a BA and draft HGMP to NMFS for review and comment. A program for systematic monitoring of the status of Chinook salmon in the basin was put in place and executed by ODFW under contract with the COE. The key issues specific to the McKenzie River identified in the BA and subsequent responses from NMFS were the following:

• Provide fish passage for Chinook salmon at Cougar Dam to reestablish the South Fork run.

• Modify the release of water from the project dams to reduce impact upon spawning and rearing of salmon below the dams.

• Reduce genetic introgression (interbreeding) between wild and hatchery stock. At that time the plan was to capture all hatchery-origin fish that did not return to the hatchery before they could cross Leaburg Dam into the upper river, thereby creating a “wild fish sanctuary” for native spawners above the dam.

• Create a systematic monitoring program consistent with the ESA requirements. This would include fin clipping, and later otolith marking to confirm whether a fish was truly naturally spawned even if it appeared not to be clipped.

• Based on new standards for reducing potential impact of gene exchange between wild and hatchery stocks, increase the incorporation of wild spawners to about 20% of the broodstock (i.e., create an “integrated” hatchery stock).

The various agencies’ responses to these requirements were at best mixed. Some progress was made in setting new standards for release of water from project dams, and a monitoring program was initiated to track the status of native spawning Chinook and the numbers of hatchery fish that escaped to spawn. However, there was no tangible progress in establishing fish passage at Cougar Dam. The newly-implemented monitoring program documented that the level of genetic introgression continued to be unacceptably high. The number of wild Chinook continued a downward trend. On the administrative side, NMFS had not accepted the originally submitted BA, and there was no HGMP agreed to by all the participating parties.

As a result of this lack of progress, in 2007 the Willamette Riverkeepers and the Northwest Environmental Defense Center filed a complaint in federal court contending that the involved federal agencies were in violation of the ESA for not completing the required program documents or actuating the programs. In early 2008, the agencies settled the case, with NMFS agreeing to produce a Biological Opinion (BiOp) in response to the various drafts of HGMPs; that the COE would proceed with their Cougar passage project; and the effort to reduce genetic introgression by removing hatchery strays at Leaburg Dam was to proceed. This resulted in an Upper Willamette Basin 2008 BiOp from NMFS which stated the action items and timelines for completion, and the COE produced a new BA because the prior document wasnow obsolete. Notably, the issues and their proposed solutions did not change much from what had been discussed during the previous 8 years, though the data accumulated over this time reinforced the need for action.

In 2011 NMFS and ODFW produced a document entitled “Upper Willamette River Conservation and Recovery Plan for Chinook Salmon and Steelhead” (, which generally covered the requirements of the BiOp but largely omitted firm time frames for achieving these goals, or penalties for failing to do so. During their preparation of public comments on this document, the McKenzie Flyfishers and Steamboaters became concerned by the lack of progress on implementing actions specified in either the 2008 BiOp or the 2007 settlement agreement. For instance, while the BiOp stated that the percentage of hatchery origin spawners (pHOS) in the McKenzie River should be < 10%, the observed values consistently averaged around 40% or more for the river below Cougar Dam; and the major plan for reducing pHOS, involving installation of a hatchery/wild fish sorter at Leaburg Dam, had been abandoned as infeasible. Further, the dates set by the 2008 BiOp for downstream passage of fish spawning above Cougar Dam had come and gone; and the program for incorporating native spawned Chinook into the hatchery broodstock was not being followed.

Equally concerning was the lack of any credible programmatic response to a rapidly evolving scientific literature demonstrating the surprisingly severe impact of hatchery origin fish spawning in the wild, or to new molecular tools for monitoring these effects on natural populations. For example, recent papers have raised serious questions regarding the ability of “integrated” hatchery practices to avoid reduction in reproductive performance among wild spawners. (See for example, Chilcote, M. W., K. W. Goodson, and M. R. Falcy. 2011. “Reduced Recruitment Performance in Natural Populations of Anadromous Salmonids Associated with Hatchery-Reared Fish.” Canadian Journal of Fisheries and Aquatic Sciences 68 (3):511–22. doi:10.1139/F10-168.) One conclusion that can be drawn from this analysis is that the effective population size (Ne) of naturally spawning salmonids is substantially smaller than the total number of spawners. This subject warrants considerably more analysis but it should caution us that just counting redds and carcasses may substantially misstate what is going on in the rivers and mask issue which arise from small breeding populations (e.g., inbreeding, allele loss and adaptation to changing environments). (Allendorf, Luikart Aitken, 2013)

Based upon the above information, we concluded that continued high levels of genetic introgression could threaten the viability of the McKenzie River Chinook ESU regardless of prior assessments of this risk. Following discussions with each of the agencies involved in managing this fishery, and with support from the Western Environmental Law Center, in December 2013 the McKenzie Flyfishers and Steamboaters filed a complaint in Federal Court alleging that the COE and ODFW were in violation of the ESA and its associated administrative requirements. The complaint alleged that the agencies operated the McKenzie Hatchery for years without an approved HGMP; allowed a genetic introgression level of at least four times the limit set by NMFS; and failed to establish fish passage at Cougar Dam, despite the requirements set out in the 2008 BiOp. The plaintiffs asked for a summary judgment barring the release of more than the number of Chinook smolts needed for conservation purposes (reestablishing a spawning population above Cougar Dam) until there was an approved HGMP defining the scope of the program. The matter was set for a settlement conference in June 2014. That process resulted in the COE and the plaintiffs agreeing to an immediate three-fold reduction in Chinook smolts released into the McKenzie River, the COE’s submission of an updated HGMP for the McKenzie Hatchery to NMFS within 45 days, and their final decision on the program for fish passage at Cougar Dam no later than March 2015.

However, ODFW refused to settle the case and it ultimately went before a federal judge in Eugene, Oregon at a hearing on March 2, 2015. The judge’s ruling, released on March 13, denied the plaintiffs’ request for summary judgment and injunctive relief, on the grounds that there had been correspondence between ODFW and NMFS indicating that the latter found ODFW’s proposed program appropriate appropriate, and thus ODFW was protected from liability. Based on this reasoning, the court also accepted ODFW’s right to release the 605,000 smolts that they were proposing. This number effectively cuts the smolt release number in half from the historic program levels, and should have some positive effect on reducing genetic introgression. Importantly, however, the court also affirmed, as did the court in the similar Sandy River Case, that the evidence accepted by all parties clearly confirms that genetic introgression between hatchery origin and wild fish of the same species harms the latter. Further, the judge ruled that the target set in the 2008 BiOp for the maximum acceptable genetic introgression, as measured by the pHOS proxy, must be met in a reasonable time frame acceptable to the court. Specifically his order states that “…the defendants need to understand that this may not be kicked down the road endlessly. Accordingly, the court intends to oversee this process to ensure that the target is met in a realistic time frame.” The court stated that its ruling in favor of ODFW is “contingent upon defendants consulting with NMFS to establish a time frame for defendants to achieve a less than ten percent pHOS and submitting a proposal of the deadline to this court for approval. Defendants have ninety days to submit the proposal to the court.”

We are disappointed that the court did not find ODFW liable for ESA violations, but feel that the court’s finding that genetic introgression is harmful to endangered fish is an important precedent, with implications for many issues involving anadromous fish. We are also gratified that the court is maintaining jurisdiction over the development of critical corrective actions to the management of this fishery. At the same time, we observe that the COE has not yet announced a decision on whether to complete a project for downstream fish passage at Cougar Dam, despite the commitment they made in the 2014 settlement agreement. Also, ODFW recently submitted its own HGMP for the McKenzie Hatchery independent of the COE, even though COE owns the hatchery and has always been regarded as the agency primarily responsible for HGMP submissions. COE has objected to the approval of such a document, asserting that ODFW has no standing in the process. We are currently monitoring the situation.

Today it’s generally agreed that, of the various stocks of Chinook salmon in the Upper Willamette Basin, it’s likely that only the Clackamas and McKenzie River stocks are sufficiently productive to avoid extirpation; and that the McKenzie River population is the most genetically intact and most likely to be the source of recovery of these iconic wild fish. Sadly, although the conservation value of these fish is unquestioned, the escapement has continued to drop over the past 12 years and in 2014 was at the lowest number of natural spawners ever observed on the McKenzie River.

Bibliography of Citations:

Araki, H., and C. Schmidt. 2010. Is Hatchery Stocking a help or harm? Evidence, limitations and future directions in ecological and genetic surveys. Aquaculture 308:S2-S11.

Allendorf, F.W., G. Luikart and S.N. Aitken. 2013. Conservation and the Genetics of Populations, 2nd Ed. Willey-Blackwell, Chichester, U.K. (See Chapters 6-8 and 14-18).

Join the Movement.

Help us protect our precious watersheds with your support.

Become a Member