Klamath River Update – March 2024

On March 2, CDFW reported the mortality of recently released (Feb. 28) salmon fry from the new Fall Creek Salmon Hatchery located on a Klamath River tributary upstream of the site of the recently removed Iron Gate Dam. The Iron Gate Hatchery located at the foot of the dam site was removed with the dam and replaced by the Fall Creek Hatchery. Mortality of the salmon fry was attributed to gas bubble disease caused by the fry passing through the Iron Gate Dam release tunnel.

Iron Gate Reservoir and the three upstream reservoirs were emptied beginning on January 11 prior to dam removal. As the reservoirs were drained, the gage below Copco Dam picked up a large increase in turbidity with an associated complete loss of dissolved oxygen (Figure 1). Oxygen returned to the water after several days despite continued high turbidity. This indicated the initial dissolved oxygen loss was likely related to the flush of organic sediment from the bottom of the reservoirs as the draining neared completion. After the flows stabilized (Figure 2) and water level in the river had dropped six feet by the end of January, turbidity dropped and stabilized near 3000 mg/l suspended sediment, and normal high dissolved oxygen returned. Turbidity was measured using three parameters (Figure 3).

The hatchery salmon fry released on February 28 were subjected to a Klamath River with elevated turbidity (suspended sediment concentrations above 2000 mg/l). Such concentrations for extended exposure (days) are highly detrimental to salmon fry.1 The combination of high suspended sediment and gas bubble disease likely has contributed to poor juvenile salmon production this year in the lower Klamath River.

The removal of the Klamath River dams will have substantial long-term benefits for salmonids. As the dam removal process proceeds, it is important to mitigate the short-term impacts of high turbidity levels to the degree possible. Continuing high turbidity events (see March levels in Figure 3) do not bode well for hatchery or wild salmon in the Klamath this year. With nearly 4 million juvenile Chinook salmon yet to be released from the Fall Creek Hatchery this year, it would be wise to either wait for next fall to release them or truck the smolts to the Klamath estuary.

Figure 1. Water level, suspended sediment, and dissolved oxygen in the Klamath River above Iron Gate Reservoir and mouth of Fall Creek, January 16 to March 10, 2024.

Figure 2. Streamflow below the Iron Gate Dam site January 1 to March 10, 2024. Source: USGS.

Figure 3. Suspended sediment and turbidity upstream of Iron Gate Reservoir above the mouth of Fall Creek near Copco, January 16 to March 10, 2024.

  1. Newcombe, C.P., and J.O.T. Jensen. 1996. Channel suspended sediment and fisheries: a synthesis for quantitative assessment of risk and impact. North American Journal of Fisheries Management. 16:693-727.

Catch-and-Release and Mark-Selective Fisheries Providing Salmon for the Future

Current proposals by various governmental officials and agencies are not adequate to protect public trust fisheries. The Central Valley fall-run salmon escapement fell below 100,000 in 2022, levels not seen since the 2008 and 2009 drought (Figure 1). Spawning numbers in the upper mainstem Sacramento River near Redding were below 5000 in 2022, record low levels also not seen since 2016 and 2017 (Figure 2). Fall-run salmon escapement numbers for the entire Sacramento River showed a similar pattern (Figure 3). Salmon fisheries were closed in 2009 and 2023 to ensure against over-fishing.

The upper mainstem fall-run salmon population was historically the backbone of Central Valley salmon escapement and fisheries. That population and its natural-born component has crashed and is need of immediate attention. Otherwise, hatcheries will be shut down, no fisheries will be allowed to protect wild fish, and salmon will go the way of the condor. Aggressive action is needed to save the salmon and salmon fisheries.

In a December 2023 post, I suggested California adopt mark-selective salmon fisheries – harvest of only hatchery fish and catch-and-release of unmarked wild and hatchery fish (only about 25% of hatchery smolts are marked). This would protect wild salmon and allow harvest of hatchery salmon. It is a strategy that is now commonplace in the Pacific Northwest. 1

Informal feedback on the suggestion has been mostly negative.  Commercial fishermen really don’t like the idea, because they would prefer a quota.  Otherwise, they would have high bycatch mortality (20+%) of wild or unmarked fish.  They already kill too many undersized fish that they have to release.  Sport fishermen have similar concerns, although they admit they use gear and techniques that have lower release mortality.  Fisheries agencies simply don’t like the added management problems.  In the end, all these entities would rather close the fishery down next year and let the stocks rebuild.  However, the rebuilding will take years.  Many hatchery salmon will go to waste.

There is a solution that would allow salmon fisheries without driving wild salmon populations to extinction.  All hatchery smolts should be marked to differentiate them from wild (natural-born) salmon. The practice would allow mark-selective fisheries.  All hatchery smolts should also be transported to the Bay or coast for release.  This would ensure high hatchery smolt survival and relieve the competition with wild fish in rearing and migrating reaches of the rivers and Bay-Delta estuary.  It would also likely reduce predation on wild juvenile salmon in the rivers and Bay-Delta estuary, because hatchery smolts in rivers and the estuary attract predators.

To participate in the fishery, commercial and sport fishermen would have to modify gear and methods to reduce bycatch mortality.  Agencies would have to provide more education/information, rules, and more monitoring and assessment.  Through information gathering and experience, it may be possible to focus fishery effort toward areas and times more frequented by hatchery salmon and where bycatch mortality is minimal.  With these additions, the fisheries agencies could focus more on wild salmon recovery, while ensuring the hatchery program and its fisheries are efficient and effective.

Figure 1. Total escapement of four salmon runs in the Central Valley 1975-2022.

Figure 2. Upper Sacramento River Fall-Run Salmon escapement from 1952-2022. Coleman is hatchery counts. Others are mainstem and upper Sacramento River tributary spawning surveys.

Figure 3. Sacramento River Fall-Run Salmon escapement from 1975-2022.

Trucking Central Valley Salmon Smolts from Hatcheries to Salt Water

A November 1, 2023 article, originally published in High Country News and later posted in Maven’s Notebook, describes the practice of trucking juvenile salmon from hatcheries for release in salt water as a “culprit,” stating: 

According to a growing body of scientific evidence, it’s also the reason that many salmon are getting lost on their way back to their birth rivers, placing the future resilience of the species at risk…. These trucked hatchery fish may survive longer in the short term, but they will return to the river system years later with massive gaps in their memory and little sense of how to locate their spawning grounds. Instead, many end up wandering up unfamiliar rivers or streams and spawning far from home.

What the article doesn’t say is that juvenile salmon released directly in San Francisco Bay or San Pablo Bay, or in the ocean, are as much as ten to a hundred times more likely to live to spawn as are juvenile fish released near their hatcheries of origin.

It is true that trucked hatchery salmon smolts have a higher “straying” rate than smolts that are released near the hatcheries in which they were raised.  Sometimes, that difference in straying is quite dramatic.

On the other hand, while straying does cause salmon to wander into Central Valley rivers other than those from which they came, most of the rivers to which they stray would have few if any salmon at all if it were not for these strays.  And right now, trucking is necessary for the water projects to meet their mitigation goals of putting salmon back into the ocean to sustain salmon fisheries.

Furthermore, if it were not for trucking, the investment of hundreds of millions of dollars in salmon hatcheries would largely be for naught.  Only in wetter years do releases of hatchery-raised salmon near the hatcheries come anywhere close to achieving hatchery production goals.  In the drier years, when hatcheries provide their greatest benefit, very few fish released at or near the hatcheries survive downstream migration through Central Valley rivers and the Bay-Delta.

Trucking also reduces the competition between hatchery smolts and wild fish for limited habitat downstream of the Valley’s rim dams.

Below, I provide examples of straying rates for the Mokelumne Hatchery and Coleman Hatchery, from which some of the highest percentages of straying occurs.  The American and Feather River hatchery releases also have elevated straying of trucked smolts, but at much lower rates.

Mokelumne River Hatchery Straying

One of the greatest straying problems is from the Mokelumne Hatchery smolt releases, especially in drought years.  The Mokelumne Hatchery trucks more smolts percentage-wise than the other six salmon hatcheries.  However, coastal releases of Mokelumne Hatchery fish in drought years 2014 and 2015 yielded returns of 0.79-1.15% compared to 0.01% from the river release below the hatchery (Table 1).

However, straying rates for coast releases were greater than 50% to other rivers and hatcheries compared to 0% for the Mokelumne River releases (Figures 1-4).

Table 1.  Mokelumne Hatchery selected release groups – number and survival rates

 Coleman (Battle Creek) Hatchery Straying

Coleman Hatchery smolts trucked to the Bay have a much greater rate of straying than smolts released near the hatchery near the mouth of Battle Creek near Redding (Figures 5 and 6).  However, smolts released near the hatchery have a much lower survival/return rate (Table 2).

Table 2.  Coleman Hatchery selected release groups – number and survival rates.

Stray Counting

Other than showing up in these figures, strays are not accounted for in escapement estimates for individual rivers, and they are not counted in return tabulations of their hatchery of origin.  Fish counted at a hatchery or in river surveys simply get accounted for in the escapement estimate for the river to which they return.  As an example, tabulations for returns to the American River (Figure 7) show that in 2015, about a quarter of the tabulated escapement originally came as strays from the Mokelumne Hatchery.

Conclusion

It is good practice to reduce straying of hatchery salmon.  But in my view, arguments about straying often tend to obscure, not improve, the problems of poor survival of both wild and hatchery salmon in dry years due to inadequate flow and other aspects of poor water management.  And as long as commercial and sport salmon fisheries in California and Oregon are substantially dependent on hatchery production in the Central Valley, it makes a lot of sense to prioritize the survival to adulthood of hatchery salmon over their fidelity to natal rivers and streams.

For more on the trucking of juvenile hatchery production, see: https://calsport.org/fisheriesblog/?s=trucking&submit=Search

Figure 1. Returns from a Mokelumne Hatchery release to Golden Gate in 2014. Yellow dot is hatchery location. Green dot is release location.

Figure 2. Returns from Mokelumne Hatchery release to Santa Cruz Harbor in 2014.

Figure 3. Returns from Mokelumne Hatchery release to Moss Landing in Monterey Bay in 2015.

Figure 4. Returns from Mokelumne Hatchery release to lower Mokelumne River in 2014.

Figure 5. Coleman Hatchery 2014 smolt release group returns. Green dot is release site.

Figure 6. Coleman Hatchery 2014 smolt release group returns. Green dot is release site.

Figure 7. Green wedges are proportion of tags recovered in the American River in 2015 whose origin was the Mokelumne River Hatchery. Source: Pacific Fisheries Management Council.

How to Not Close Salmon Fisheries

California salmon fisheries do not have to close. Hatcheries in California are still releasing thirty million hatchery smolts each year. This means that three to five hundred thousand adult hatchery salmon are still out there for potential harvest. About a quarter of the fish released from hatcheries are marked. Selectively harvesting the marked hatchery fish, while returning to the water all unmarked fish that are caught, is reasonable.

Marking all the hatchery smolts would quadruple the number of harvestable fish.

Do not let anyone tell you this is not reasonable. The state and federal governments have mismanaged California’s natural salmon production nearly into oblivion. They can spend the money to partially mitigate the consequences by marking all hatchery fish.

two fish photo, showing fin removal

Photo of marked and unmarked hatchery fish. Photo credit: Idaho Dept. of Fish and Wildlife. In the Columbia basin, all hatchery salmon are marked, and thus hatchery fish and wild fish are immediately distinguishable.

For more information on mark selective fisheries see:

https://wdfw.wa.gov/sites/default/files/publications/02353/wdfw02353.pdf

 

Guest Blog: Salmon Declines and Hatchery Options

(Editor’s Note: From time to time, the California Fisheries Blog gets requests for guest posts. We like to accommodate requests for posts that we feel, at our sole discretion, are substantive and thought-provoking. Though we discourage pseudonyms, we may, as here, allow posts without attribution when such posts allow a platform to speak out for persons who are professionally constrained. We reserve the right to edit guest posts for clarity. As with all posts on the California Fisheries Blog, guest posts do not represent the policy or opinions of CSPA.)

By “Kilgore Trout”

On Saturday (March 18, 2023), Sep Hendrickson’s “California Sportsmen” radio show hosted James Stone, current president of the Nor-Cal Guides and Sportsmen’s Association. The Association recently lobbied to close the California salmon fishing season for 2023. The discussion raised several interesting issues about the status and management of salmon.

Mr. Stone questioned why regulators did not close the salmon fishery earlier than this year. He noted that in 6 of the last 8 years, the annual escapement of Sacramento fall-run Chinook salmon was below the minimum conservation objective of 122,000 adults, a dismal 75% failure rate for forecasters.

As background, the Sacramento fall-run Chinook is the dominant salmon population commercially fished offshore of California. The population is an aggregate of hatchery and natural production, dominated by hatchery production. A year’s escapement is the abundance of adults that return (in the fall) to spawn in the Sacramento River, its tributaries, and hatcheries. The following spring, the fall-run Chinook offspring of natural-origin emerge from the gravel, smolt, and migrate seaward; the hatchery-origin fish artificially produced by broodstock matings are fed and reared as fry and smolts (in raceways or ponds), then released near the hatchery, or trucked to the estuary or Bay for release.

Sep and James agreed that all too often, 100% of California’s recent salmon declines are blamed on climate change and droughts, not factors like overfishing after years of low escapement. Indeed, a NOAA study conducted after the 2008 closure of the California salmon fishery attributed the collapse primarily to poor ocean conditions, but also noted contributing factors like dry inland conditions and fishing.

Sep and James continued to discuss water management in California’s Central Valley. James reminded listeners that California’s Fish and Game Code 5937 requires dam operators to release water to protect fish. This is correct, and it seems that conservation objectives for salmon (like suitable river temperatures and minimum escapement numbers) should be established to account for environmental variations like hot summers and dry winters that contribute to poor brood years. What’s the point of establishing salmon protections if we scream “Emergency!” and toss protections aside whenever consecutive dry years put agricultural or municipal water users in a short-term bind?

But water management to conserve salmon is not as simple as host Sep Hendrickson framed it when he contended, “There is water behind dams that is oxygenated that can be added and cool at any time they want to; they choose not to.” There isn’t always enough water, and it’s not as simple as saying that politicians simply choose not to release it from dams.

Salmon juveniles emerging from the gravel near Redding must travel hundreds of river miles downstream, where they enter and transit the Delta and Bay to reach the Pacific. That means the Sacramento River must be cold enough for salmon from Redding to the Bay. At the same time, water is released from reservoir storage for agricultural and municipal uses. For there to be enough cold water in the bottom strata of Shasta Reservoir to cool the Sacramento River for salmon, water released from the reservoir in any year must both keep the river cold and retain enough water in storage so that it stays cold later in the year. Shasta’s operators must also retain enough water in storage to allow cold water management in the following year if the following year is dry.

There isn’t space here for a full discussion of Sacramento River water supply and use, or the constraints on achieving temperature (and other) requirements for salmon. This would involve considering complex topics like salmon biology, climate, flood control, drought management, federal water contracts, State water rights, Delta salinity, ocean conditions, and others. But the issues are more complex than politicians (like our Governor) simply choosing not to release water for salmon.

Recognizing the gravity of the Sacramento fall-run Chinook collapse, James Stone warned, “If we don’t raise more hatchery fish, we could possibly lose the fall run forever.” Sep Hendrickson responded, “We need a state-of-the-art hatchery. We can do this state with one hatchery, centrally located that handles everything…” James Stone told listeners they could join the Nor-Cal Guides and Sportsmen’s Association, which has lobbied since 2019 for funds (up to $100 million) for a new hatchery on the mainstem Sacramento River. Stone described it as a modern facility that would allow the trucking of fish and the return of fish, and help protect our stocks for many years. The hatchery’s objective would be to “re-colonize and re-populate the Sacramento River with hatchery fish” and “get them to spawn in the rivers and start reproducing the natural spawn.” Stone added that a healthy river is the best hatchery because it could produce millions more salmon eggs than a hatchery.

Getting funds could help if the objective of “…reproducing the natural spawn” could be achieved by supplementing the production of natural-origin salmon in the Sacramento River watershed.  But would another large, production hatchery “reproduce” the natural spawn, or hasten its replacement?

After all, hatcheries in the Sacramento River watershed already produce and release millions of Sacramento fall-run Chinook. The Coleman National Fish Hatchery (Battle Creek) releases 12 million fall-run Chinook smolts annually. The Feather River Hatchery has an annual goal to release 6 million smolts, and the Nimbus Fish Hatchery (American River) another 4 million. Other Central Valley hatcheries not in the Sacramento River watershed also release fall-run Chinook. The goal of the Mokelumne River Fish Hatchery is to release 5 million smolts, with an additional 2 million released into San Pablo Bay or into acclimation pens in the ocean. The Feather River Hatchery also produces an additional 2 million fall-run Chinook to truck downstream for an ocean enhancement program. Before building another large hatchery, it seems fair to ask why releasing millions of hatchery fall-run Chinook – year after year – hasn’t already reproduced the natural spawn.

What if current hatchery practices are also exerting negative effects on Sacramento fall-run Chinook, like overfishing and unbalanced water management do? Yes, some California hatchery facilities are very old, but what if investing $100 million to bring them to state-of-the-art production levels makes at least some things worse?

Ditto for building “one hatchery, centrally located that handles everything…” We already know that very little population structure remains in the Sacramento fall-run Chinook; the variation or diversity that once existed has been greatly diminished from the time when they thrived not only in the Sacramento River, but also in large tributaries like the Feather, Yuba, and American rivers, and in numerous other smaller rivers and streams in the watershed. Large dams that eliminated nearly all the upstream natal habitat of the winter-run and spring-run Chinook are generally regarded as the primary cause of the demise of these stocks. But the dams did not eliminate nearly as much fall-run Chinook habitat because the fall-run do not migrate as far upstream to spawn. So, relative to habitat loss due to dams, did hatcheries play a larger role in the “homogenization” observed in the fall-run Chinook stock?

We know that salmon in streams do not select mates randomly, so the random mate selection in hatcheries effectively eliminates adult competition. We also know that captive rearing and feeding of juvenile salmon minimizes the mortality that would naturally occur in a river. Do juvenile salmon in hatchery ponds acquire food or avoid predators the same as fish in the wild? It also makes sense that wild juveniles migrating hundreds of miles in a river must adapt to more perilous environments than do hatchery fish transported in trucks. Are the consequences of these hatchery effects the losses of vigor, the ability to adapt to local environments and variation, and evolutionary fitness?

It seems we could better understand hatchery effects by spending some of the $100 million on modern salmon monitoring. Genetics-based tools already exist, so that all hatchery broodstock can be tissue-sampled and genotyped, with the information stored in a computer database. All hatchery offspring (millions of fish) would be effectively “tagged” and their hatchery of origin could be identified later, if they are genotyped when captured — in the fishery, after straying to the natural spawning grounds, when interbreeding with wild fish, etc. Similarly, tissues from salmon carcasses on the natural spawning grounds could be collected and genotyped (they are already surveyed every year by the California Department of Fish and Wildlife). This process would genetically “tag” the natural-born offspring in the Sacramento River and its tributaries.

These tools would allow biologists and managers to know the origin of a salmon. They could also better understand the effects of artificial propagation, such as interbreeding, on natural-origin fish. We could begin to understand if hatcheries could “re-colonize and re-populate the Sacramento River with hatchery fish” and “get them to spawn in the rivers and start reproducing the natural spawn.”

An alternative to building and ramping up another large production hatchery might be  to try (mobile) conservation hatchery set-ups, to temporarily supplement wild stocks in the Sacramento River and tributaries. With genetic tagging, we could know how well the offspring survive to return and spawn, and how successful their offspring are at surviving and reproducing. We could detect if and when the rivers get healthier, and begin producing more eggs and adult salmon than the hatcheries do. We might get to a place where there is no need to clip adipose fins.

Let’s start working together to recover salmon!