Author Archives: Tom Cannon

Salmon in 2024

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Salmon in the ocean off the coast of California in 2024 will consist primarily of Central Valley hatchery fish ages two, three, and four.  They were released primarily as sub-yearling smolts in 2021, 2022, and 2023 (born in the fall of broodyears 2020, 2021, and 2022 respectively).

Feather River Hatchery

The Feather River Hatchery released approximately 8 to 10 million fall-run salmon smolts in the spring of each release year.  All were trucked to the Bay or coast, except for 1.5 million released to the lower Feather River in April of wet year 2023.  My guess is that the number of the fishable salmon in the ocean that are 2-to-4-year-old fall-run Feather hatchery fish could be 500,000 fish in 2024, with 125,000 marked with an adipose fin clip.  The hatchery also released another 6 million spring-run smolts in the three years – all marked.  The total marked salmon in the 2024 fishable stock will likely be about 150,000.

American River Hatchery

The Nimbus Hatchery released 4 to 5 million fall-run smolts per year from 2021 to 2023.  Nearly all were trucked to the Bay or coast.  My guess is that about 50,000 of Nimbus broodyear 2020-2022 marked salmon will be in the fishable stock in 2024.

Mokelumne River Hatchery

The Mokelumne Hatchery released approximately 6 million fall-run smolts per year from 2021 to 2023.  Nearly all were trucked to the Bay or coast.  My guess is that about 100,000 of Mokelumne broodyear 2020-2022 marked salmon will be in the fishable stock in 2024.

Coleman (Battle Creek) Hatchery

The Coleman Hatchery released approximately 10-12 million fall-run smolts per year from 2021 to 2023.  Nearly all were released at or near the hatchery.  My guess is that about 25,000 of Coleman broodyear 2020-2022 marked salmon will be in the fishable stock in 2024.

Other Central Valley Salmon Hatcheries

The three smaller salmon hatcheries release about one million salmon smolts per year near the hatcheries, about half of which are marked.  My guess is that about 5,000 of broodyear 2020-2022 marked salmon from these hatcheries will be in the fishable stock in 2024.

Klamath/Trinity Salmon Hatcheries

Klamath/Trinity has two hatcheries that release a total of 4-5 million smolts per year.  I have not included them in this assessment.

Summary

My guess is that there will be about 330,000 marked hatchery salmon from the Central Valley salmon hatcheries in the 2024 fishable stock, not counting Klamath/Trinity or Oregon/Washington marked stocks that occur in small numbers off the California Coast.  The number is similar in size to the NMFS/PFMC Sacramento Index that is the basis of salmon harvest management for coastal and inland salmon harvest (see chart below).  Though the estimates are complicated and only crudely comparable, they are a reasonable basis for developing a 2024 fishery harvest strategy.

Recommendation

I suggest a harvest of up to 200,000 of the marked salmon only in a California mark-selective fishery in 2024.  That is a total harvest similar to the average over the past decade, but with protection built in to minimize harvest of wild, natural born (unmarked) salmon and the unmarked portion of hatchery releases.  There is concern for marked listed hatchery winter-run and spring-run salmon that would need consideration, but these fish are generally protected through seasonal and area restrictions.  Regulations and monitoring specific to a mark-selective fishery would have to be put in place.  Experience in the Pacific Northwest indicates mark-selective fisheries are a viable alternative to closed fisheries.

Status of Winter Run Chinook Salmon in the Sacramento River – A Poor 2023 Run

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The latest carcass count survey indicates another near-record low-run of winter-run salmon in the upper Sacramento River in 2023 (Figure 1). Most of the spawning occurred in June and July 2023 (Figure 2). The official total winter-run escapement includes hatchery returns, Battle Creek counts, and fishery harvest, but is not available yet for 2023 (Figure 3). The low 2023 spawning census count can be directly attributable to broodyear 2020’s poor spawning, incubation, rearing and emigration conditions in below normal water years 2020 and critically dry year 2021.1

Broodyear 2020 started as eggs and milt in their parents in winter-spring of 2020. They were spawned and hatched in summer 2020. They began moving downstream in late fall 2020, rearing and emigrating in the lower river and Bay-Delta, and finally reaching the Bay and ocean in winter-spring of critically dry year 2021. The juveniles that survived returned as three-year-olds in winter-spring of 2023.2 Broodyear 2021 (two-year-olds in the 2023 run) were also subjected to drought conditions, spawning, rearing, and emigrating in 2021 and 2022 before returning in 2023.

Major stresses on young broodyear 2020 salmon included:

1. Broodyear 2020 spawners and their eggs and embryos were subjected to less-than-optimal water temperatures during the May-August 2020 spawning season (Figures 4 and 5).

2. Flows remained very low from September 2020 through January 2021 (Figure 6). Water temperatures were also stressful during fall 2020 (see Figure 5). Without flow pulses in fall and winter, young winter-run salmon survival was poor (Figure 7), with delayed emigration (Figure 8).

Major stresses on adult salmon from broodyear 2020 that returned to spawn in 2023 included:

3. Upon returning in spring 2023 to spawn, broodyear 2020 adults were subjected to stressful water temperatures in May and June in the lower Sacramento River (Figure 9).

4. During the adult winter immigration period, two two-week-long flood events resulted in about half the Sacramento River flow passing into the Sutter and Yolo Bypass via overflow weirs (Figure 10). Large numbers of adult winter-run from broodyear 2020 were likely attracted into the flow from these bypasses. Those passing upstream via the bypass channels are subject to being blocked at the overflow weirs or stranded in bypass channels. Large fish passage “notches” are currently being constructed at the larger Tisdale and Fremont Weirs, but they are not expected to be operational until late in 2023 at the earliest. Large numbers of adult winter-run from broodyear 2020 were likely lost in the bypasses in winter 2023, as they were in past wet years.

In summary, poor numbers of winter-run broodyear 2020 spawners returned to the Sacramento River in 2023 despite the fact that the ocean and river salmon fisherieswere closed under an emergency order. The low numbers of spawners is attributable to poor river conditions in 2020 during spawning, rearing, and emigration, and in 2023 during the adult run up the Sacramento River in winter-spring.

Figure 1. Winter-run salmon carcass counts in spawning reach near Redding from 2003-2023. Five lowest tallies occurred two years after critical drought years 2008, 2009, 2014, 2015, and 2021. Source: USBR

Figure 2. Carcass counts by calendar week in 2023. Peak counts were in July (weeks 27-30). Source: USBR

Figure 2. Carcass counts by calendar week in 2023. Peak counts were in July (weeks 27-30). Source: USBR

Figure 3. Winter-run salmon escapement includes the carcass survey, hatchery returns, and Battle Creek returns. Source: CDFW GrandTab.

Figure 4. Water temperature in the Sacramento River in 2020 below Keswick Dam and above the mouth of Clear Creek – the upper ten miles of river in which winter-run salmon spawn. Red line is recommended water temperature threshold for these locations for salmon spawning and egg incubation. Source: www.cbr.washington.edu/sacramento/

Figure 5. Threshold analysis for 2020 in upper Sacramento River. KWK=Keswick Dam. SAC=Redding. CCR=Above Clear Creek. BSF=Balls Ferry. JLF=Jelly’s Ferry. BND=Bend Bridge. Source

Figure 6. Lower Sacramento River flow rate September 2020 to March 2021.

Figure 7. Broodyear index for winter-run salmon young catch at Knights Landing rotary screw trap 2008-2023. Source

Figure 8. Tisdale screw trap collections of winter run smolts in fall-winter of water year 2021. Source

Figure 9. Water temperature in upper Sacramento River at Red Bluff and lower Sacramento River at Wilkins Slough April-July 2023. Red line is target threshold water temperature for winter-spring migrating adult salmon. Source

Figure 10. Water flow through three Sacramento Flood Control Weirs in 2023. TIS=Tisdale. CLW=Colusa. FRE=Fremont.

Table 1. Winter-run salmon hatchery releases percent survival for 2009, 2014, 2015, and 2016 release-year tag groups. Most returns occur at age three two years after release. Note low survival from 2009 releases (<0.03%), 2014 releases (0.03-0.18%), and 2015 releases (0.10-0.21%) in critical drought water years. Higher survival rates (0.40-0.81%) occurred from 2016 releases in a normal water year.

  1. A small portion of the spawners in any year are two-year old jacks and jills. ↩
  2. A few remain in the ocean and may return as 4-yr-olds in 2024. ↩

Why Does the Mokelumne River Hatchery Have a Record Salmon Run this Fall 2023 when Runs at the Battle Creek (Coleman) Fish Hatchery Are at Record Lows?

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Water Year 2023 (10/1/22-9/30/23) in the Central Valley was very wet, with exceptional hydrology. With the state’s salmon fishery closed and plentiful water there had been some optimism for the 2023 salmon runs. But there was also concern as to how much this year’s salmon runs would be affected by the poor water years 2020-2022.

The Mokelumne River system is achieving hoped-for outcomes from its salmon management. Over 20,000 salmon adult salmon have been counted moving upstream past the Woodbridge counting facility. The counting facility on Battle Creek has counted only about 5,000 salmon, in a system whose adult return are generally far greater than those on the Mokelumne. What happened?

  1. Reasons for Strong Run in Mokelumne River – News reports and interviews with hatchery managers indicate a record high escapement of fall-run salmon to the Mokelumne River and hatchery. Factors that likely contributed to the strong run include the following:
    1. Of the 21 million fall-run smolts produced and released by the Mokelumne Hatchery during drought years 2020-2022, about half were released to coastal harbors and half released to Sherman Island sites on the lower San Joaquin River channel in the Delta (Table 1). These releases likely made up the vast majority of Mokelumne River returns in 2023 of age 2-4 adult returns.1 Past survival rates for such coastal and Delta releases are among the highest for Central Valley hatchery fall-run salmon smolt releases. Coastal releases regularly have survival rates 5 times the rates of the Delta releases and 10 or more times the rates of Mokelumne River in-river releases. No releases were made to the Mokelumne River below the hatchery from 2020-2022. Straying rates of adults returning from the Mokelumne Hatchery off-site smolt releases often exceed 50%, with most going to the American River and lesser amount returning to the Feather and Merced rivers. Strays from hatcheries on those rivers also return to the Mokelumne River.
      b. The Mokelumne River has prescribed summer-fall attraction flows for fall-run salmon (Figure 1). However small in magnitude, they seem to attract adult salmon.

  2. Reasons for Poor Winter-Run and Fall-Run Salmon Runs in Upper Mainstem Sacramento River and Battle Creek – News reports and hatchery news releases indicate a very low run for salmon in Battle Creek and the upper Sacramento River in 2023.
    1. a. All hatchery smolt releases from the Coleman Fish Hatchery on Battle Creek and the Livingston Stone Fish Hatchery on the Sacramento River in Redding in 2020-2022 were to the upper river near the two hatcheries. In prior years, survival was low for river releases in drought years and higher for Bay-Delta releases (Table 2).
    2. River conditions in the Sacramento River are generally poor (high water temperatures and low flows) in drought years like 2021 for late winter and early spring hatchery releases and wild salmon emigration. Overall outmigration success in every year but one has been poor since 2008, and is trending downward (Figure 2). However, in late winter and early spring 2021, a natural flow pulse occurred in the upper river that helped move the hatchery and wild smolts downstream (Figures 3 and 4).
    3. Water temperatures in the lower reaches of the Sacramento River were high when adult salmon were migrating upstream towards the upper Sacramento River and Battle Creek (and hatchery) (Figure 5).

Table 1. Tag groups of Mokelumne Hatchery fall-run smolts released in spring by location in 2020-2022 (brood years 2019-2021).

Figure 1. Streamflow of lower Mokelumne River at Woodbridge gage in water years 2020-2022 and long term average. Note October attraction flows and winter pulse flows.

Table 2. Survival table for selected winter-run and fall-run smolt release groups from the Livingston Stone Hatchery and Coleman Hatchery during critical drought years 2009, 2044, 2015 and normal year 2016.

Figure 2. Broodyear index for juvenile fall-run salmon catch in the lower Sacramento River at Knights Landing rotary screw trap 2008-2023. Source

Figure 3. Water temperature and streamflow in the lower Sacramento River at Wilkins Slough in March-April 2021. Red outline is period of (upstream) Coleman Hatchery smolt releases.

 

Figure 4. Tisdale screw trap collections of winter-run smolts in the lower Sacramento River in fall-winter of water year 2021. Source

Figure 5. Water temperatures in the lower Sacramento River at Wilkins Slough and Freeport during adult salmon immigration period in 2023. Green line represents safe level for adult migration. Yellow line is stress level and water quality standard. Red line is high stress and avoidance level.

  1. Only partial 2020-2022 returns have been recorded for broodyear 2019 releases on the RIMS code-wire-tag database. Two-year old returns appear complete and show over 50% of returns to river-hatchery escapement was to the American River, particularly Nimbus Hatchery. ↩

Spring Run Salmon Collapse 2023

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The National Marine Fisheries Service (NMFS), in an  August 2023 Assessment, provided a status review of spring-run Chinook salmon in California’s Central Valley.  The Assessment found that salmon are declining, but primarily as part of a short-term trend, under the burden of climate change.

The conclusions of the August Assessment stand in stark contrast to October’s condor-like effort to preserve remaining wild spring-run salmon in a conservation hatchery at UC Davis.  This contrast demonstrates the limitations of the federal and state resource agencies’ focus on climate change and the ocean as the cause of the salmon declines and the reason to shut down fisheries.1 The resource agencies need to direct more attention to controllable elements: water operations.  On that level, they must take immediate action, before another one of California’s most important public trust resources is lost.

Quotes from NMFS’ 2023 Update to the Viability Assessment for Spring-Run Chinook, and Comments

Populations in many ESUs declined in abundance compared to the previous review five years ago. In most cases, these declines appear to be caused by variation in survival rates in the ocean environment. In the coming decades, climate change, including negative effects in the ocean, is expected to be a major factor impacting Pacific salmon (Crozier et al. 2019). In the near term, however, we generally viewed the recent declines as mostly being short-term and not necessarily indicative of a major underlying change in ESU/DPS status. Several populations within each ESU/DPS were evaluated to have a declining trend in overall viability (i.e., increased extinction risk) since the last review. …  No new information suggests that the delineation of the CVSRC ESU should change at this time. (p. 2) [emphasis added]

Comment:  I generally disagree with NMFS’s conclusions, because these conclusions do not reflect the reality of effects of the 2013-2015 drought or the more recent 2021-2022 drought.  NMFS predicted these effects in its 2016 review, particularly the effects on the freshwater river and estuary habitat conditions, and the roles played by state and federal water management.  Thiamine Deficiency continues to be the theory driving NMFS’s focus on the ocean.  However, NMFS has not addressed alternative theories that water management in freshwater exacerbates the effects of the lower thiamine that stems from ocean feeding on anchovies.

As to the statements that recent declines are “near-term” and that “no new” information warrants a change in the level of risk status for Central Valley spring-run, one must assume that NMFS regrets these conclusions in light of the catastrophic numbers of spring-run spawners in September and October of 2023.

Climate plays an important role in salmon (Oncorhynchus spp.) habitat at every stage of their lifecycle. For instance, predictable seasonal climate variations interact with the physiography of salmon watersheds to provide predictable seasonally varying water temperature and streamflow regimes that create diverse life-history pathways for different salmon populations of the same and different species. Likewise, irregular climate and weather variations like persistent drought, episodic floods, or persistent marine heatwaves, can impact salmon populations by altering their aquatic habitats and food-webs, which in turn affect individual salmon growth and survival rates in ways that can impact salmon populations at local to regional scales. Climate variations impacting regions across 100s to 1000s of kilometers can thus impact ESU/DPS viability through impacts on abundance, productivity, spatial diversity, and distribution. (p. 6) 

Comment:  Water management in the Central Valley can also be a major problem, if not the main problem.  NMFS holds some of the responsibility for this water management, but continues to avoid it.  Yes, droughts have been frequent, but the effects of droughts on salmon have gotten worse because of drought-year water management.  NMFS’s role in 2013-2015 and in 2021-2022 was to quietly acquiesce to the California State Water Resources Control Board’s decisions to grant the requests of state and federal agencies to weaken flow and temperature requirements during drought conditions.

It is NMFS’s responsibility to oppose the federal agencies’ requests to weaken standards during droughts.  Such requests are federal actions.  NMFS continues to act as though it has no authority over the Bureau of Reclamation’s deliveries of water from Shasta and Trinity reservoir water to California’s water contractors.  But these deliveries are most certainly federal actions that require NMFS’s review and approval under the Endangered Species Act (ESA).

The period of 2013–2021 has been exceptional for its high frequency and magnitude of West Coast drought and terrestrial heat, widespread and severe wildfire, and record-setting marine heatwaves in the California Current Large Marine Ecosystem and broader northeast Pacific Ocean. Climate extremes from 2013–2021 have contributed to extreme bottlenecks in West Coast salmon survival rates for multiple West Coast salmon populations and subsequent declines in abundance for many DPSs and ESUs.  (p. 6)

Comment:  While poor ocean conditions may have been a major part of the problem in 2008-2009, this was not the case in the 2013-2021 period, at least in terms of the Central Valley salmon.  NMFS needs to look closer to home to address the causes and solutions to the Central Valley salmon collapse.

Trucking Central Valley Salmon Smolts from Hatcheries to Salt Water

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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.