Author Archives: Tom Cannon

Salmon Have Already Been Compromised in Wet 2023

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Warming water in the Sacramento River in late April compromised salmon as rains diminished and Central Valley water managers captured snowmelt for storage and irrigation. The water warmed as wild juvenile salmon and 20 million or so hatchery smolts moved down the Sacramento River toward the ocean, and as adult winter-run and spring-run salmon migrated up the river.

Water temperatures increased despite a clear trajectory toward full reservoirs (Figure 1). Water temperatures at Wilkins Slough rose nearly 10oF in late April to the low 60’s, while flows dropped from March flows of 25,000 cfs to only 12,000 cfs during the April hot spell (Figure 2). Though prescribed small flow pulses from Shasta Dam1 (Figure 3) and cool weather (Figure 4) reduced thermal impacts in early May, that was not true for the end of April.

Allowing flows to drop and water temperatures to rise in the last half of April was irresponsible and easily avoidable. Releases from storage to keep the river cool would not have even come close to preventing Shasta from filling. The goal for the lower Sacramento River to minimize stress on migrating juvenile and adult salmon in a wet year like 2023 should be water temperatures below 60oF (Figure 5).

Water managers need to manage for fish at the same time they manage for water supply, not as an afterthought. In a year of abundant water, active management for fish is not that hard and has no water cost. Even in less bountiful water years, the mindset and bias of filling before releasing requires adjustment.

Figure. 1. Shasta has dramatically filled this spring.

Figure 2. Streamflow and water temperature in the lower Sacramento River at Wilkins Slough in 2023.

Figure 3. End of April flow pulse from Keswick Dam near Redding.

Figure 4. Air temperatures at Red Bluff in 2023.

Figure 5. Interagency water temperature prescriptions for salmon recovery from the San Joaquin River Salmon Recovery Program.

California Needs a Wild Salmon Policy

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Canada has a Wild Salmon Policy. California needs one. California can develop a better salmon policy by taking a good look at the Canadian policy.

In past posts, I have mentioned the need for a comprehensive California Salmon Plan.1 There are many plans in California, but there are few with real actions like NOAA Fisheries (National Marine Fisheries Service – NMFS) Central Valley Salmon Recovery Plan. The problem is that most plans have no “bite.” NMFS has been given a “bite option” in issuing take permits under the Endangered Species Act, but NMFS rarely uses its full authority in issuing biological opinions for federal projects. NMFS is particularly averse to issuing “jeopardy” opinions with mandated Reasonable Prudent Alternatives (RPAs).

Canada’s Wild Salmon Policy2

“Wild salmon hold tremendous value for natural ecosystems, cultural and spiritual practices, jobs and income, and recreational enjoyment along the coast and inland watersheds of the Pacific Region. They are important for Indigenous people, communities, individuals, groups and businesses.” (Policy, p. 5).

The value of California’s wild salmon public trust resources needs more consideration and recognition. For example: in setting rules for commercial and recreational harvest of the dominant fall-run Chinook salmon stocks, little or no consideration is given to protecting dwindling wild fall-run salmon populations.

While Canada’s Wild Salmon Policy is not exactly a plan with specific actions (the Policy leaves that to local and regional entities), the Policy does outline goals, objectives, strategies, approaches, and what might be called overarching concerns. Chief among the Wild Salmon Policy’s overarching concerns that also apply to California salmon are:

  • Diversity – There were once many salmon stocks located within and among the many rivers and tributary streams in the Central Valley. Preserving this genetic diversity deserves much more consideration.
  • Keystone species – Maintaining the role of salmon that were once important to the entire ecosystem, bringing in marine nutrients and carbon to watersheds, is important.
  •  Declines in specific populations – There is a need to immediately address sudden or unforeseen drops in abundance of any population or subpopulation.
  • Ocean and river conditions – There is a need to recognize and react to sudden or unforeseen changes in habitat conditions that have potential adverse impacts to salmon.
  • Less predictable returns – Accurate predictions are real problems for fishery managers; poor predictions are the norm.
  • Reduced available stocks for harvest – There is a need to anticipate and address stock collapses before and after they occur through aggressive planning and an array of actions; lower fishable stocks threaten traditional uses of public trust resources like salmon.

Canada’s Wild Salmon Policy has three main strategies:

  1. Involve stakeholders – Stakeholders have unique and important knowledge about Pacific salmon, how the local environment functions, and characteristic ecological relationships.
  2. Develop technical methods and tools – To support the status assessment of salmon conservation units, there must be initiatives to assess habitat and ecosystems, and day-to-day fishery and ecosystem management decisions within regional programs that reflect the principles, goals, and objectives of an overall wild salmon program.
  3. Develop and implement a comprehensive management plan – Canada uses a comprehensive plan with a five-year implementation plan and an annual-review process. (Note: the latest 5-Year Winter-Run Salmon Plan in California was dated 2016.)

The general approach of Canada’s Wild Salmon Policy is:

  • Engage partners and stakeholders at the local level to leverage local knowledge and expertise.
  • Facilitate collaboration through salmon governance processes and capacity building.
  • Consider guiding principles and objectives in ongoing management and program activities, both internally and with partners.
  • Adapt and update best practices based on lessons learned.

The strategies for and approaches to assessment in Canada’s Wild Salmon Policy are:

  • Standardized monitoring of wild salmon – To understand the current status of wild salmon stocks, it is important to have regular, standardized, science-based monitoring that identifies benchmarks for Conservation Units (CUs).
  • Determine the current status of Conservation Units.
  • Continue to monitor and assess status of Conservation Units.
  • Set Priorities – Implement prioritization method for assessing and monitoring Conservation Units or groups of Conservation Units.
  • Modify or develop metrics and document new status assessment methods.
  • Consolidate and improve documentation of standards for internal and external monitoring programs and improve data sharing through open processes.
  • Consider guiding principles and objectives in planning annual and multi-year work processes.
  • Continue integrated planning discussions through various mechanisms, including local roundtables.
  • Work on an integrated approach to wild salmon.

The delineation of Conservation Units and their benchmarks does not prescribe specific management actions, but rather is used to inform decision-making. As spawner abundance (escapement) decreases, a Conservation Unit moves towards a lower status, and the extent of management intervention for conservation purposes increases. A low Conservation Unit index is undesirable because of the risk of extirpation and the loss of ecological benefits and salmon production. Changes in status should trigger management actions, which will vary depending on species, geographic regions, and cause of the decline.

The implementation Plan of Canada’s Wild Salmon Policy involves:

  • Assessment of impacts and monitoring habitats.
  • Accountability in completing actions and reporting.
  • Maintaining and rebuilding salmon populations.

In conclusion, Canada’s Wild Salmon Policy provides a good model for a badly needed comprehensive Central Valley Salmon and Steelhead Protection and Recovery Plan or Program, for the entire array of federal and state salmon and steelhead projects that are undertaken in the Central Valley. It should encompass planned and ongoing projects funded by the departments of the Interior, Commerce, Agriculture, Defense, Energy, and by the EPA, as well as those jointly permitted by the California Resources Agency.

How to Not Close Salmon Fisheries

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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

 

With Salmon Season Closed for 2023, the Work is Just Beginning

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The final rules adopted by NOAA Fisheries and California Department of Fish and Wildlife this spring will be much different than last year’s rules.  The 2023 commercial and sport fishing closure is designed to ensure that adequate numbers of fall run salmon, the primary stock of the fishery, return to spawn this year and  begin the recovery of the population to allow future fisheries.  The Pacific Fisheries Management Council (PFMC) and the California Fish and Game Commission are taking this extreme action as their authorized contribution to the recovery of collapsed California’s salmon populations.  This year’s salmon closure follows yet another three-year drought (2020-2022) and associated water mismanagement.

But the work does not stop at closing the season.  The legal authorities of other state and federal agencies must now kick in and do their part.  With the salmon out in the ocean now protected, the next steps are to protect broodyear 2022 that is now in the rivers and the Bay-Delta estuary, and to be ready for the return of remaining broodyear 2019 and broodyear 2020 and 2021 adult salmon that will re-enter fresh water to spawn this fall and next year.

Hatchery Production

There are 20 million or so fall-run salmon pre-smolts soon to be released this spring from the seven Central Valley salmon hatcheries.  Hatchery personnel will release these salmon to the rivers, Delta, Bay, and coast.  Where and when they do so will greatly affect how many salmon reach the ocean and return to the rivers to spawn (escapement).

The following measures if adopted will increase success:

  • Truck as many smolts as possible to the coast and Golden Gate. Hold as many as these as possible for late spring, summer, and late fall (yearling) release.
  • Limit in-Delta and East Bay releases, because to succeed they must occur in early spring when receiving waters are cool. Early spring releases are smaller fish that do not survive as well, especially if they are released near the hatcheries.
  • Coordinate river (near-hatchery) releases in spring with river and Delta inflow/outflow flow pulses and with optimal water temperature and turbidity conditions.
  • Appropriately clip all adipose fins, and coded-wire tag all smolts.
  • Track and analyze survival under varying release strategies.
  • Adopt a Parental-Based-Tagging (PBT) program to support the overall recovery program.
  • Fund and implement hatchery program facilities and operational improvements, as recommended and planned by agencies.

Natural Production

Millions of eggs will be spawned in rivers this fall, despite what may be a near-record-low number of returning adults (escapement) in 2023.  It is imperative that the young salmon hatched from these eggs survive and contribute a maximum of natural-born smolts to the ocean.  We are so lucky that Mother Nature has provided the necessary water resources this year to allow that to happen.

As it is, only 32,000 adult salmon spawned naturally in rivers last fall, compared to 300,000 just a decade ago.  The earlier 2010-2016 recovery was a great accomplishment soon after the 2007-2009 population crash, when natural born escapement was only 25,000-70,000 (see Table 1).  That recovery was brought about after two years of fisheries closures (2008-2009) and three relatively abundant water years (2010-2012).

The following measures if adopted will increase success:

  • Provide coordinated spring river flow pulses with storage reservoir releases and/or foregone water diversions (if necessary).
  • Maintain minimum flows in rivers to meet or exceed year-round water temperature standards.
  • Limit south Delta exports during natural or induced flow pulses, and otherwise follow the export restrictions required in the 2008-2009 Biological Opinion.
  • Minimize salmon egg, embryo, and fry stranding in spawning gravel beds (redds) that occur when reservoir releases are reduced after spawning has occurred.
  • Minimize stranding, entrainment, or adverse water temperature changes caused by otherwise legal water diversions.
  • Limit agricultural or municipal waste water discharges that may increase water temperature in key salmon habitats.
  • Upgrade gravel supplies in prime spawning habitats before next fall’s spawning season.

Future Fisheries

In addition to closing fisheries and limiting harvest this year, it will likely be necessary to limit harvest in 2024 and 2025.  This is because of the over-harvest in 2021 and 2022 of broodyears 2018 and 2019 (Figure 1), which will likely lead to poor returns from broodyears 2021 and 2022 (Figure 2).  Broodyear 2021 is of special concern, because, like broodyear 2020 (whose poor prognosis for 2023 escapement led to the fishery closure), broodyear 2021 reared and out-migrated in a critical drought year (2022).

The following measures if adopted will increase success:

  • Plan for a closure in 2024 to protect an expected poor return from broodyear 2021.
  • Consider as an option for the 2024 and 2025 seasons a mark-selective fishery if the measures under Hatchery Production outlined above are accomplished and show signs of being effective.

Other recommended actions

https://www.fisheries.noaa.gov/feature-story/endangered-salmon-regain-access-healthy-west-coast-habitat-through-20-projects-funded

https://wildlife.ca.gov/News/cdfw-announces-225-million-to-benefit-salmon-and-support-critical-habitat-projects-statewide#gsc.tab=0

Chinook escapement in Sacramento River

Table 1. Source: PFMC.

Graph of Sacramento Index from 1983 through 2022

Figure 1. Sacramento River fall-run Chinook salmon population index comprised of escapement (natural areas and hatchery counts) and river and ocean harvests. (Source: PFMC)

Graph recruits versus spawners

Figure 2. Author-developed spawner-recruit relationship using total escapements in Table 1. Number shown is recruit year escapement (left y-axis is log(x) minus 4 of recruits) plotted against spawner escapement (x-axis, recruitment three years prior). Actual number is shown in log scale on right y-axis. Red lines are target PFMC escapement range for fishery. Red and blue circles show recruitment difference between wet and dry years at maximum sustained yield spawner levels. (Spawner levels of 300-500 thousand levels can yield 500,000 recruits from wet years or as few as 100,000 recruits from dry years). Note poor recruitment in 2021 and even less in dry year 2022 due to over-harvest.

 

 

Yuba River Fall Run Salmon – Status Winter 2023

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When I last assessed the status of the fall-run salmon population of the Yuba River near Marysville in a 1/31/22 post, I stated: “The population remains in a very poor state – at about 10% of recent historical levels during and subsequent to multiyear droughts 2007-2009 and 2013-2015 (Figure 1).” Since the record low run in 2017, the fall run on the Yuba River has not recovered.

The failure of the four more recent runs to show signs of recovery (Figure 1) is especially concerning because 2017 and 2019 were wet years. The failure to recover may be simply the lingering effects of the drought years 2014-2015 and the ongoing effects of the 2021-2022 drought. More likely, the spawning stock has collapsed and is in dire need of support. The 2022 run appears to be even worse than the past four runs,1 thus adding to the concern.

This post delves into the many possible causes of, or contributors to, the collapse of the Yuba River fall-run salmon population. The story is a complicated one. It starts with broodyear 2014.

Graph from 1953 though 2021

Figure 1. Yuba River fall-run salmon spawning escapement estimates 1953-2021. (Data source: GrandTab)

The first stop in pursuit of the potential causes of the recruitment failure that has occurred not only on the Yuba River, but in most of the other Central Valley fall-run salmon populations, is a close look at the escapement data.  The spawner-recruitment relationship (S/R) shown in the escapement data (Figure 2) provides a closer perspective than the simple histogram of the run sizes (Figure 1).

The S/R figure is a plot of the log of the escapement with the log of the escapement three years earlier. This is because about 80-90% of spawners are three years old.  The three red lines in Figure 2 show that adult spawners in 2014 produced the spawners 2017, which in turn produced the spawners in 2020.  The adult spawners in 2018 produced the spawners in 2021.  Spawners in 2019 produced spawners in 2022, which based on the incidental reports will likely show up to the lower left of 19.  The lower-left quadrant of an S/R plot is usually a place where a salmon population is headed toward collapse and an inability to sustain itself.

Graph of Spawners versus Recruits

Figure 2. Yuba River fall-run salmon spawner-recruit relationship (1978-2021) with recruit number shown in chart for specific years. Red lines point from spawner to recruit year. For example, recruits in 2017 led to recruits in 2020. Recruits in 2014 (12,000) led to only 1500 in 2017.

When Yuba River escapement (recruitment) is adjusted for strays from other rivers, the recruitment level in record low 2017 (Figure 3) shows itself to be even more dire.  The Yuba River receives many strays because it carries a strong cold-water signal into the Feather River and on into the lower Sacramento River in late summer and early fall.  The Yuba River also attracts spring-run and late-fall-run hatchery salmon that are included in the Yuba River’s fall-run spawning counts.

It is helpful to start the analysis of the 2017 population crash by reviewing the early life cycle of broodyear 2014 – as eggs in their mothers.  Their parental stock, broodyear 2011, had been reasonably normal, if not in the range that might be considered the Maximum Sustained Yield 10,000-15,000 (Figures 1 and 2).  The strong numbers of broodyear 2011 spawners (and their broodyear 2014 eggs) arrived in the Bay in summer 2014.  The questions become what happened to:

  1. those broodyear 2011 adult females;
  2. their broodyear 2014 eggs and their hatchlings in summer-fall 2014;
  3. the surviving broodyear 2014 fry in winter 2015; and smolts in spring 2015;
  4. the yearlings, two-year-olds and three-year-olds in the ocean; and finally
  5. the adults making up the 2017 run counted in the Yuba River spawning grounds.

The answer is that survival conditions were not good for all five categories above.  Each question is addressed below.

Two graphs

Figure 3. Yuba River escapement numbers. Source: PFMC 22, p.49.

1. The first question addresses the conditions that faced broodyear 2014 eggs when they entered the Golden Gate inside their broodyear 2011 mothers that fateful summer of 2014. Water-year 2014 was a critical drought year, during which the State Board weakened Delta water quality standards for the year.

    • Unusually warm water met the salmon when they entered the Bay in summer of drought year 2014 (Figure 4). By the time they reached the mouth of the Feather River at Verona (if they got that far), water temperatures were near the lethal 75º F level through September (Figure 5).  Elevated water temperatures occurred through the entire route from the Golden Gate to the Yuba River.
    • Once on the spawning grounds of the, Yuba the parents of broodyear 2014 eggs encountered drought-year low flows (Figure 6), which in addition to being warm provided minimal available spawning habitat quantity and quality.
    • By the time the parents were ready to spawn in early fall, they were likely compromised by disease and thiamine deficiency, limiting the viability and survival of the broodyear 2014 eggs, and thereby the potential reproductive success of broodyear 2014 and its contribution toward 2017 recruitment.

2. The second question addresses the subsequent fate of surviving broodyear 2014 eggs and the hatched alevins in gravel redds. The eggs and alevins in the spawning beds faced unusual stresses in the form of erratic flow and very low flows (Figure 7).  Eggs spawned in October-November were subjected to scouring flows in December.  Eggs spawned in December under the high flows were subsequently subject to dewatering in January.

Graph water temprature versus time

Figure 4. Water temperature in San Francisco Bay spring-summer 2014.

Graph of water temperature versus time

Figure 5. Water temperature in Sacramento River below mouth of the Feather River at Verona gage July-October 2014.

Graph of Daily Discharge in 2014

Figure 6. Streamflow in Yuba River at Smartsville and Marysville gages July-October 2014.

Discharge Graph 2014

Figure 7. Yuba River streamflow in water year 2015 and 53-year average at Marysville gage.

3. The third question addresses conditions in the late fall through spring in critical drought water year 2015. Emergent fry likely benefitted from the February flow pulse that facilitated some fry movement out of the Yuba toward the Delta (see Figure 7).  Those fry that did not move were then subjected to extremely low flows (and stressful water temperatures) through the spring in the lower Yuba River and the lower Sacramento River below the mouth of the Feather River (Figure 8).  Delta and then Bay conditions were at their worst for young Yuba salmon on their way to the ocean in the spring of drought year 2015, made worse by the State Board’s continued weakening of water quality standards.

Graph of discharge in 2015

Figure 8. Streamflow and water temperature in the lower Sacramento River below the mouth of the Feather River at Verona gage in winter-spring 2015.

4. The fourth question regarding broodyear 2014 addresses growth in the ocean from 2015 through early summer 2017. In the ocean, they were subjected to strong fishery pressure (Figure 9) in all three years by the commercial and sport fisheries.  This provokes a series of questions.  Why did the Pacific Fisheries Management Council or PFMC allow those 50%+ harvests after the 2008-2009 collapse and fishery closures, and lack of subsequent population recovery?  Had the fall-run salmon populations really recovered sufficiently to sustain 50%+ harvests?  How accurate were those harvest rate estimates?  How hard were the stocks being preyed upon by seals and orcas?  Were the salmon whose diet had largely consisted only of anchovies becoming thiamine deficient by the time they spawned in the Yuba in early fall 2017.  In considering all these questions, one can only conclude that the summer upstream migration of fall-run salmon to the Yuba in 2017 had been highly compromised before it started.

5. The fifth and final question regarding broodyear 2014 salmon addresses conditions adult fish faced when they re-entered fresh to spawn after having been subjected to high harvest rates in the ocean from 2015-2017 (implied in Figure 9).  Upon returning to the Bay in summer 2017, a wet year, they encountered much better conditions during their upstream migration and spawning period.  After a final tweak by the summer river fishery, they spawned in the Yuba River in record low numbers.

Nearly identical circumstances and outcomes occurred with broodyear 2015 in 2018 (see Figure 3).  Broodyears 2016-2019 were subject to similar stresses.  Broodyears 2020 and 2021 were subject in-river to critical drought years 2021 and 2022.

In conclusion, it appears that the damage to broodyear 2014 and broodyear 2015 had been done for the most part by the time they returned as adults to the Bay in 2017 and 2018.  The record-low numbers of spawners estimated from the carcass surveys in 2017 and 2018 (Figure 1 and 2) were the cumulative effect of a series of survival factors, beginning with stresses on their parents in drought years 2014 and 2015, and ending with high harvest rates in the ocean and rivers in 2017 and 2018.  Management decisions by the State Board and PFMC, with acquiescence by federal and state resources agencies, contributed to this fateful series of events.  The events and their consequences were predictable, and the State Board and PFMC should have anticipated them and taken appropriate measures at the time.

It appears the same mistakes were made in regard to broodyears 2016-2021.  The effects of drought in years 2021 and 2022 will likely contribute further to the crash of the Yuba River salmon population, with even lower Yuba River and Central Valley salmon escapement in 2023-2025.

For more on the problems faced by Yuba River fall-run salmon and what can be done about them, see this October 2018 post.

Figure 9. Sacramento River fall-run salmon index 1983-2019. The 122 on y-axis is the target starting population level (122,000) under which harvest is allowed. Note the fisheries were closed in 2008 and 2009. Source: PFMC.