The Continuing Quest for McKenzie River Wild Chinook Salmon Recovery

By Dave Thomas and Arlen Thomason

The McKenzie River originates in the high lava bed aquifer atop the Oregon Cascade Mountains. The rushing, crystalline water of its upper 13 miles is designated a federal Wild and Scenic river, after which the gradient gradually declines as the river traverses forests and farm lands, and eventually merges into the larger Willamette River in Eugene, Oregon. Along the way it is fed by many small streams and several major tributaries, the largest being the South Fork. It supports several species of salmonids, most notably Chinook salmon. Large runs of spring Chinook salmon had been returning to the McKenzie since well before Europeans settled in the region. Early settlers reported numerous spawners throughout the river.

But as we documented in the May 2015 issue of The Osprey (“McKenzie River Chinook Salmon: A Legacy Population in Peril” (https://www.ospreysteelhead.org/archives), there has been a steady and steep decline in the Upper Willamette Basin spring Chinook salmon population over the twentieth century, and well into the twenty-first.

It was designated as threatened with extinction under the federal Endangered Species Act (ESA) in 1999. Since then the descent has continued, with only the McKenzie River population remaining large and genetically intact enough to be considered by fishery ued to drop to dangerously low levels over the last few decades.

Threats To Mckenzie Chinook Salmon Survival

managers as a “legacy” or “stronghold” population, potentially capable of seeding recovery within the entire Upper Willamette basin. Yet the McKenzie salmon population itself has also contin-

There are likely multiple factors responsible for this decline, including harvest, habitat loss and degradation, ocean conditions, migration-blocking dams, and counter-intuitively, salmon hatchery programs. Historical channelization of the originally braided McKenzie River, as well as development along its banks—particularly on the lower river—undoubtedly contributed to reducing good spawning areas and salmon production potential. Three dams—Trail Bridge, Cougar, and Blue River—built on the upper McKenzie and its major tributaries in the middle of the last century cut off access to an estimated 22% of some of the best spawning habitat. And as wild salmon populations dropped, government agencies responded by releasing ever more hatchery salmon into the river, reaching a peak of about 1.2 million smolts annually over the period of 1999-2011.

In our May 2015 article we focused primarily on the damage that hatchery salmon are likely exerting on their wild counterparts in the McKenzie River, particularly by interbreeding with them and transferring potentially maladaptive, deleterious genetic traits for optimal survival and reproduction in the natural environment. Part of the reason for that focus was that while habitat restoration and dam modification for fish passage are critically important for population expansion, they are also generally big, difficult, expensive, and long-term projects. Whereas addressing hatchery fish interbreeding is potentially much easier, cheaper and quicker. All it takes is a management (or court) decision to STOP doing something: releasing so many hatchery smolts into the river. Nearly everyone involved agrees that high levels of hatchery/wild salmon interbreeding— as measured by the surrogate metric

Continued on next page

“Proportion of Hatchery Origin Spawners”, or pHOS—may play a role in salmon survival. High pHOS values, at 10% or above, is a bad thing for wild salmon; and agencies are in fact mandated to keep it below that number. For more background on the history of the river, management actions, and the role of pHOS, the reader is referred to our 2015 article linked above.

For the purposes of this article, it is important to know that production of hatchery salmon for the McKenzie River has two stated purposes: (1) for outplanting in the South Fork above Cougar Dam, where some of them may spawn and produce out-migrating offspring, for the conservation objective of eventually restoring a viable, selfsustaining Chinook salmon run to this tributary; and (2) providing a salmon fishery in the lower McKenzie River, as well as in downstream rivers and the Pacific ocean.

Mckenzie Salmon Population Status At Year End 2022

Hatchery Management

Following the litigation against the United States Army Corps of Engineers (“the Corps”) and Oregon Department of Fish and Wildlife (ODFW) and the court decisions described in our 2015 article, the court maintained jurisdiction and oversight of the process until the required Hatchery Genetic and Management Plan (HGMP) was approved in 2019. And no more than the reduced number of 604,750 smolts have been released since 2015. Those facts notwithstanding, it can be fairly argued that at least until 2022, the very elevated pHOS problem continued to be kicked down the road, as the numbers remained at historical high levels. Moreover, the HGMP directed that beginning in 2018, 3-year rolling pHOS assessments would be conducted, and management adjustments made if the < 10% target was not met. To date no such formal administrative assessments have been conducted nor adjustments made; it does not appear that any are currently planned; and no public comment about it has been forthcoming.

The graph below shows the pHOS values for 2002-2021 for the entire McKenzie River. In every year since 2014, the year prior to our last article, and two years after the Corps and ODFW initi-

McKenzie River pHOS 2002-2021

ated some steps to reduce pHOS the number has been well above the <10% target. There has been no downward trend over this period. In fact, due largely to a water supply failure at the McKenzie Hatchery beginning in late 2018, the pHOS numbers spiked higher in 2019 and beyond. However, due to a successful hatchery salmon trapping and removal operation at Leaburg Dam in 2022, pHOS values in the river above the dam are expected to be very low for that year. We don’t yet know what to expect for pHOS values for the entire river. Spawning survey results for 2022 should be made public in spring 2023. See the section “2018 Leaburg Canal Shutdown and McKenzie Hatchery Water Loss”, below, for more information about this critically important issue.

Numbers of Returning Adult Wild Salmon

At the time of our last writing, the latest available data (2014) for wild Chinook salmon returning to the McKenzie River at Leaburg Dam had reached an all time low of about 1,000 fish. This alarming low point was the culmination of a persistent, decade-long decline from almost 6,000 fish in 2003, and there were concerns that it was headed still lower. But as can be seen in the graph below, it now appears that as of 2022 the population numbers have been more or less stable since about 2008, at around 1,600 fish with a standard deviation of about 485. So while this low number is still very concerning, it appears that for now the population may

Continued on next page be at least holding steady. Of course, holding steady is not the goal. The ESA requires that actions be taken to ensure that threatened and endangered species be recovered to the point where they no longer need ESA protection. Since the approval of the HGMP and the commitment of the Corps to implement fish passage at Cougar Dam and take other related actions, the available data does not reflect any progress in recovery of McKenzie Chinook salmon.

Key Developments Since 2015

2018 Leaburg Canal Shutdown and McKenzie Hatchery Water Loss

McKenzie Hatchery is located about 2 miles below Leaburg Dam, which is owned and operated by a public utility, Eugene Water and Electric Board (EWEB). This is a low-head dam, established in 1929 to divert water into the approximately five-mile-long Leaburg Canal, extending downstream, above and roughly parallel to the river.

Very importantly, most of the water needed to operate McKenzie Hatchery is provided by Leaburg Canal. In October 2018, the hatchery suddenly lost that water. Longstanding leaks in the canal wall had become worse, and fearing a catastrophic failure that could cause a disastrous flood, the Federal Energy Regulatory Commission (FERC) had ordered that the canal be drained and shut down until the problem was thoroughly assessed and fixed. It has since become clear that the canal problem and its potential remedies are major, complex, tremendously expensive, and long-term. (See “Outlook for the Future”, below, for more details.)

Loss of its water supply was catastrophic for the hatchery, and for Chinook salmon pHOS levels in the McKenzie River. Without water to run through the hatchery and down its ladder to the river, there was no way for adult salmon to return to it. Beginning in the summer and fall of 2019, the vast majority of returning adult hatchery salmon remained in the river, where they could spawn with wild salmon. As a result, pHOS levels for the river over the next few years were among the highest in history.

Finding an alternate way to capture returning hatchery salmon and remove them from the river became an urgent priority. In 2019 ODFW took the initia- tive to expand its ability to selectively trap and remove hatchery salmon (while allowing wild salmon to pass) at one of the ladders near the left bank of Leaburg Dam, to lower pHOS and to at least prevent them from reaching the most productive spawning grounds above the dam, where most wild salmon spawning occurs. A prototype manually-controlled sorter/trap was put in place late in the run of 2020. Improvements were made to the sorter and its operation in 2021.

In 2022 the operation of the sorter was further improved, and critically, the right bank ladder was modified so that adult salmon could not ascend it; thus all salmon going upstream had to pass through the left bank sorter. Altogether, these modifications made a big difference, and almost all hatchery salmon trying to get above the dam were sorted, trapped and removed. Whereas the number of wild salmon counted passing above the dam was 1,854, only 49 hatchery fish managed to get by the sorter. If confirmed by spawning survey results, that would translate to a pHOS value above the dam of about 3%, by far the lowest value in history. Considering the long record of failed attempts to appreciably lower pHOS in the river, it was an important achievement. In addition, 1,188 hatchery fish were removed from the river at the dam sorter/trap, and another 855 hatchery fish were trapped as they tried to ascend the ladder to the nearby Leaburg Hatchery; for a total of 2,043 hatchery fish removed by trapping. This was at least a step in the right direction of lowering pHOS for the entire river.

It is important to note, however, that it is currently unknown how many hatchery fish remained in the river below the dam, contributing to pHOS levels that could still be very high. It also remains unknown how many wild salmon may have been discouraged by the sorting regime from crossing the dam and instead remained below it, where they would have been free to spawn with the potentially large numbers of hatchery salmon there. The pHOS mandate of <10% is for the entire river, not just the area above Leaburg Dam. Spawning survey results, expected to be available in early 2023, should shed light on these questions.

2018 Lawsuit Alleging Failure to Comply with 2008 Biological Opinion (BiOp)

In 2018 three conservation organiza- tions—Northwest Environmental Defense Center, WildEarth Guardians, and Native Fish Society—filed suit in federal court against the Corps and National Marine Fisheries Service (NMFS), alleging violations of the ESA by failure to carry out many of the actions mandated in the 2008 BiOp to reduce impacts of the Corps’ Willamette Project dams, including Cougar Dam, on ESA-listed Chinook salmon and winter steelhead. In August 2020, the court found in favor of plaintiffs on all counts. In July, 2021, the court released an order specifying what actions the defendants must take. Specifically, it ordered that the Corps and NMFS produce a new BiOp by 2024, laying out actions the agencies must complete to reduce harm to the ESA-listed fish in the Upper Willamette system.

Further, the court ordered that measures be taken immediately to prioritize water releases at several dams, including Cougar Dam, for the benefit of fish passage through and spawning below the dams. These injunction measures are temporary until the 2024 BiOp is completed, at which time the measures it contains will supersede the injunctions. For Cougar Dam, fish-prioritized drawdowns began in Nov. 2021. Preliminary tests indicated that this method of fish passage may be feasible, but injury to the fish is an issue needing resolution.

On September 7, 2020, driven by dry, unusually strong easterly winds, a wildfire sprang up near the community of Rainbow at about river mile 64; probably due to a downed power line. The fire moved rapidly west, ultimately consuming about 173,000 acres along about 34 miles of the river, and far up both sides of the watershed. It destroyed several small towns and more than 400 structures along the valley. As the fire burned extremely hot, the damage to trees, other shrubbery and even the soil was horrific in large areas. Some research by the U.S. Geological Survey indicates that loss of riparian habitat from such high severity fires can lead to higher water temperatures and increased erosion for several years or decades. Other research suggests that for less frequent and severe fires, the long term effects can actually be beneficial. It is too soon to be sure of all the effects of the Holiday Farm fire on this river corridor. While the fire undoubtedly did some damage to the riparian habitats, it is a positive sign that the spawning survey of 2021 did not show a noticeable loss in upriver redds counts. Also, while work on upriver habitat restoration began before the fire, post fire this important work seems to have accelerated. It is to this subject that we turn next.

Rewilding the McKenzie River

As noted above, the McKenzie River remains the primary refuge of spring Chinook salmon runs in the Willamette Basin, with just remnant populations in the other subbasins. This advantage is due to the unique hydrology of the river and the extent of spawning area available. However, that is not to say that the McKenzie was not subject to human actions that degraded some of the river’s spawning and rearing habitat. For instance, in places berms were built along the river that separated it from its floodplains and provided elevated platforms for riverside roads, interrupting groundwater connections and preventing small streams from accessing the river. In many places the river was intentionally channelized, to confine its water to one deeper, swifter channel while draining riverside land for other uses. The effect has been to degrade habitat for fish and other riparian biota. Over the last thirty years or so there has been increasing momentum to reverse this situation. Brief descriptions of a few of them follow.

Green Island: In 2003, the McKenzie River Trust (MRT), a non-profit organization dedicated to the protection and restoration of riparian properties in western Oregon, took control of an 865 acre farm at the confluence of the McKenzie and Willamette rivers. Reconnecting Green Island to the river by removing more than 5,600 feet of levees restored side channels, groundwater interaction and habitat with increasing richness in species for the first time in 35 years. From the salmon perspective, Green Island now represents an important rearing habitat for outmigrating juvenile salmon. More information on Green Island can be found at: https://mckenzieriver.org/property/gree n-island/

Lower South Fork: The United States Forest Service has been working to develop guidelines for habitat restoration along waterways. This work led to the creation of the Stage-0 Model of floodplain enhancement, where the zero stage represents the reach fully connected to its floodplain. For the past four years, this model formed the basis for connecting the heavily channelized lower South Fork McKenzie River (i.e, the 4.5 miles of stream below Cougar Dam to the confluence with the McKenzie River mainstem) with its historically braided valley floodplain. The result is now an increasingly well-functioning diverse habitat in a multithreaded, multi-depth waterway, spread over several hundred acres. It is already hosting new and increased animal species. But probably the most exciting aspect of the project, for those who care deeply about the river’s Chinook salmon, is that the number of spawning redds in this section of the river has increased 400% since construction was completed. Details and images of the South Fork project at: https://www.mckenziewc.org/what-wedo/restoration/, along with descriptions of similar projects in the McKenzie River basin.

Finn Rock Reach: This is a two-mile, 276-acre section on both sides of the McKenzie River just below the McKenzie South Fork described above. The section had been a lumber camp in the 1940s and later turned into a rock quarry which displaced the river’s mainstem and created berms cutting off the natural floodplain. Plans for the restoration started in 2018 when MRT raised $4.6 million dollars from the local community in support of the project. Work on the project was interrupted in 2020 as the Holiday Farm wildfire raged through the property. Since then, the work continues and staff mentioned that in the early fall their efforts were interrupted when spawning salmon showed up. Like the South Fork project, this one also appears to have great potential for increasing salmon spawning and rearing habitat in the upper river.

Outlook For The Future

Decision on Leaburg Canal Plan, Its Implementation & Effects

As described above, the Leaburg Canal was shut down due to observed structural problems in 2019. In late 2022, EWEB made the decision to partially decommission Leaburg Canal. The plan will remove part of the canal, and save part of it for stormwater conveyance from several creeks that the canal intercepted. The water previously diverted by the canal will instead remain in the river. Due to FERC requirements, the plan will also remove Leaburg Dam. Moreover, EWEB has indicated that the similar Walterville Canal, located some 10 miles downstream, will probably meet the same fate in the not too distant future. But it seems that most people who care about wild fish, ordinary citizens and agencies alike, see this decision as a win for fish.

As a consequence of this decision, it appears unlikely that Leaburg Canal will ever provide water to McKenzie Hatchery again. Further, there is no realistic prospect on the table for providing an alternate source of water to the hatchery any time soon. In addition, removal of Leaburg Dam will remove the water source for the adjacent Leaburg Hatchery as well. It will also remove the method agencies are now using to count returning salmon; to capture and remove hatchery fish from the river; and to keep hatchery fish off the upper river spawning grounds. Agencies have not yet made any specific plans for this eventuality, but clearly these developments will require hatchery management to be adjusted on the McKenzie River, if it continues at all. There will be some time to adapt, as deconstruction is unlikely to begin in less than a decade.

Cougar Dam Downstream Passage

In late 2022, the Corps released for public comment a draft Programmatic Environmental Impact Statement (PEIS) for its Willamette Valley Project dams, which proceeds along in parallel with its court-ordered new Biological Opinion due by 2024. The big news in this document, from our perspective,

Continued on next page concerns downstream passage at Cougar Dam. Since the early 2000s, the Corps has been working towards a mandated restoration of a salmon run to the South Fork McKenzie River above this dam. Until now the focus has been on building a very expensive large floating fish collector to trap young fish that make it through the reservoir to the dam, and then truck them around the dam and release them downstream. Initial smaller scale experiments were not encouraging, but the Corps stuck with that plan for years, despite lacking the funds to build it.

In the new PEIS, the Corps has proposed an annual deep drawdown of the reservoir, to a level where fish can swim out of it through a pre-existing diversion tunnel under the dam, which remains from original dam construction. This is an option that many biologists inside and outside of the Corps, including us, have favored. It appears to have a much greater chance of success, as well as being substantially cheaper and potentially quicker to implement. The nearby Fall Creek Dam has used this method successfully since 2011 (https://www.nwp.usace.army.mil/willa mette/fall-creek/drawdown/). There would still be a fair amount of work needed at Cougar Dam to make this happen. The PEIS projects that it will take until 2041 to complete this alternative, but we believe that is an unreasonably long timeline, and that feedback from other agencies and citizens during the review process could result in shortening it considerably. If this project is successful, it would reopen about 25 miles of good salmon spawning habitat that was lost when the dam was built.

Trail Bridge Dam Fish Passage Modifications

Trail Bridge Dam, owned by EWEB, is located far up the McKenzie River at about river mile 82. Built in 1963 as part of an electricity generation project, it blocks volitional access to approximately 4.4 miles of spawning, rearing, and foraging habitat for spring Chinook salmon and bull trout. As part of its relicensing agreement with multiple involved parties, and its actual license issued in 2019, EWEB committed to modify the dam to allow upstream fish passage via a trap-and-haul system, and downstream passage by modification of the dam spillway. Full implementation has been delayed as some structural problems needing correction have been found in the bottom of the reservoir behind the dam. However, a scaled down program is being put in place and both salmon and bull trout are being moved above the dam. Currently, there is no date for completion of the entire project.

Impact of Rewilding on Wild Salmon Production

The work described above for several innovative habitat improvement projects is continuing as phases are completed and new ones initiated. There are also other very promising, similar inprogress projects that we don’t have space to cover, as well as new ones in the planning stage. These include projects at Deer Creek and Quartz Creek near where they join with the upper mainstem river, as well as possible projects in places like Gate Creek. Given the initial impacts of the work on the lower South Fork on salmon productivity, this approach has the potential to yield substantial increases in the salmon population.

Impact of Climate Change on Rivers, Oceans, and Fish

Damage to the local environment that has come at the hands of humankind undoubtedly has contributed much to the decline of salmon populations. At least some of that may be reversible, by the various strategies and efforts described above. But we would be remiss if we failed to note that all of it could be overshadowed by the continuing effects of global warming, which impact not only our local rivers, but important salmon territory far beyond. Warming oceans where salmon spend most of their lives could overwhelm any local improvements, and the local conditions themselves are changing under its influence. Rivers are warming, and changing patterns of precipitation threaten water supplies. We can only hope that the larger efforts of nations and coalitions can make some progress on that front.

Parting Thoughts

A lot has happened on the McKenzie River since May 2015, as attested by the above collection of topics. There have been some disappointments, particularly the glacial pace of most government projects that were supposed to improve things, contrasting with the accelerating pace of climate change making things worse. And there were some outright calamities, like the devastating Holiday Farm wildfire, and the shutdown of Leaburg Canal with its knockon effect of leaving thousands of hatchery fish in the river to breed with wild salmon.

But there were also rays of hope. Amid the scramble by fishery managers and volunteers to corral the wayward hatchery salmon and curtail the damage, a method emerged that, at least for one year, and even if only for part of the river, yielded by far the lowest number ever of fin-clipped hatchery fish in the upper river, and lowered pHOS for the river by capturing and removing a substantial number of them.

Time will tell whether this approach, with modifications, can consistently succeed in lowering pHOS for the entire river to the mandated level, while not impeding the progress of wild salmon towards the upper spawning grounds. Even the canal failure appears to have an upside, likely leading to substantial rewatering of a significant portion of the McKenzie River. On another front, a court finally stepped up, condemned agencies’ failures to make good on their mandates and promises, and ordered immediate as well as longer term steps to do better. A late change in direction for managing downstream passage at Cougar Dam offers new hope for success. And in the habitat arena, several multi-collaborative projects between agencies and non-profits are showing great promise, already achieving milestones like increasing species diversity and strong gains in salmon redds. We look forward to seeing what comes of it all.

David Thomas is McKenzie River Steward for the Native Fish Society and a member of the McKenzie Flyfishers. A conservationist, angler and nature photographer, he trained as a population biologist and biostatistician. He taught at the University of California and later worked at NIH and in the pharmaceutical industry.

Arlen Thomason is a conservationist, author, outdoor photographer, life-long angler, and member of the McKenzie Flyfishers. He trained as a molecular biologist and worked for many years in biomedical research.