Winter-Run Salmon Update – March 2019

This post updates a 7/25/18 post on the status of the endangered winter-run Chinook salmon population of the Sacramento River. Figure 1 is an updated figure showing the influence of water supply conditions on the spawner-recruit relationship of winter-run during the recruits’ first year of life in the Sacramento River. The relationship is also influenced by hatchery contributions that began in 1998 and continue today.1 Other factors, including water temperature control improvement at Shasta Dam and changes to permits and water quality plans (not depicted), are also likely unaccounted-for factors. Figure 2 depicts raw run numbers by spawning year.

What the relationship shows is that there is a strong positive spawner-recruit relationship heavily influenced by water supply conditions and hatchery contributions. The recent estimates of >70% contribution from the hatchery to the population recruits1 reflects the importance of the hatchery role and the underlying problem of declining “wild” spawner contribution. Note that the spawner numbers for 2018 (recruits from critical year 2015 spawners) are as yet unpublished. Hatchery smolt production and releases were doubled in 2015, the third critical year of the 2013-2015 drought.

Figure 1. Spawners versus recruits (spawners three years later) transformed (logx minus 2). Year is spawner year. For example, 2014 is spawning year with 2017 recruits. Color denotes water-year type in spawning year: bold red is critical year, non-bold red is dry year, green is normal year, and blue is wet year. For example, red 13 represents critical water year 2013. Squares around numbers indicate the presence of hatchery contributions (begun in 1998).

Figure 2. Spawning population estimates of adult winter-run salmon in the upper Sacramento River from 1974 to 2017. Source: CDFW.




A Case for Winter Pulsed Flows for Winter-Run Salmon

In a December 2018 post, I discussed the need for fall pulsed flows in the Sacramento River through the Delta in dry years. In this post, I further discuss the need for winter pulsed flows, using brood years 2013-2015 and resulting rearing of winter-run salmon in drought years 2014 and 2015 and normal year 2016 as examples.

Winter-Run brood year 2013 (spawned in summer 2013) started with a good number of spawners (Figure 1), but resulted in poor escapement in 2016 (Figures 1 and 2). Likewise, brood year 2014 started with slightly fewer spawners and resulted in even lower escapement in 2017. Brood year 2015 fared better.

While the lack of fall pulse flows and poor spawning conditions and redd dewatering likely struck brood years 2013 and 2014 first, the lack of winter pulsed flows further limited their survival, or at a minimum failed to ameliorate poor fall survival. Brood year 2013 juveniles moved out of the spawning reach above Red Bluff in the fall (Figure 3). However, they did not show in traps in the lower river at the Tisdale weir near Colusa, a hundred miles downstream of Red Bluff, or at Knights Landing, further downstream, until February (Figures 4 and 5). I attribute this delay to a lack of pulsed flows to move these fish down the river. This delay in out-migration to the Bay-Delta is detrimental both to in-river survival and to the success of smolts in reaching the ocean. In contrast, brood year 2015 had significant early winter flow pulses that moved juvenile winter quickly through the lower Sacramento River (Figure 6).

One might argue that Shasta Reservoir was too low after three years of drought to provide these winter pulsed flows (Figure 7). Three days’ release of 5000-10,000 cfs would require 30,000-60,000 acre-feet of water. This is between 2.7% and 5.5% of dry-year irrigation deliveries to Sacramento River water contractors from Shasta Reservoir (1,100,000 acre-feet in 2014 and 1,200,000 acre-feet in 2015).1

Figure 1. Escapement (spawning run) numbers for winter run salmon 1974-2018. Source:

Figure 2. Spawner-recruit relationship (log10 – 2) for winter run salmon. Number represents brood year. Color represents dry (red), wet (blue) or normal (green) water year types for winter rearing/migration season following spawning. For example, 15 represents brood year 2015 under winter conditions in the normal 2016 water year.

Figure 3. Red Bluff trap catch of brood year 2013 winter run salmon juveniles fall 2013, winter 2014.

Figure 4. Tisdale Weir trap catch of brood year 2013 winter run salmon juveniles fall 2013, winter 2014.

Figure 5. Knights Landing trap catch of brood year 2013 winter run salmon juveniles fall 2013, winter 2014.

Figure 6. Red Bluff and Tisdale trap catch of brood year 2015 winter run salmon juveniles in fall 2015 and winter 2016.

Figure 7. Shasta Reservoir storage in winters 2014 and 2015. Total capacity is 4,500,000 acre-feet.




Little Action on 2014 Salmon Recovery Plan

The 2014 Recovery Plan for Central Valley salmon and steelhead includes actions designed to lead toward recovery of listed Central Valley winter and spring run salmon salmon and steelhead.  After ten years, there has been little progress and improvement, and populations are at or near record lows.  The problem is not the plan.  It is lack of implementation and progress toward implementation.  Yet despite lack of progress, various agencies are advancing new major water projects, the extension of water right permits, and the update of water quality control plans that would further threaten the state’s fishery resources if Recovery Plan actions are not implemented.

What are the key actions in the Recovery Plan whose lack of progress hinders recovery?1

  • Develop and implement an ecosystem based management approach that integrates harvest, hatchery, habitat, and water management, in consideration of ocean conditions and climate change. Such a plan, strategy, or approach does not exist.  While a comprehensive coordinated operations program exists for water supply, none exists for fisheries and aquatic resources.
  • Implement the recommendations and guidelines of the California Hatchery Scientific Review Group ( Many recommendations and guidelines have yet to be implemented.2
  • Implement and evaluate actions to minimize the adverse effects of exotic (non-native invasive) species (plants and animals) on the aquatic ecosystems used by anadromous salmonids. No progress.  Predator effects remain high from lack of adequate river flows and poor hatchery release practices.
  • Incorporate ecosystem restoration including breaching and setting back levees into Central Valley flood control plans (i.e., FloodSafe Strategic Plan and the Central Valley Flood Protection Plan). Central Valley floodplains present great opportunities as salmonid habitat. However, most of them today remain one-way detours without escape, and thus a threat to salmon.
  • Improve the timing and extent of freshwater flow to the San Francisco Bay region to the benefit of juvenile and adult salmonids by modifying water operations in the Central Valley to support flows that mimic the natural hydrograph. Water flows remain compromised and are allowed to degrade even further in droughts.
  • Develop, implement, and enforce new Delta flow objectives that mimic historic natural flow characteristics, including increased freshwater flows (from both the Sacramento and San Joaquin rivers) into and through the Delta and more natural seasonal and interannual variability. No progress, bitterly contested.
  • Reduce hydrodynamic and biological impacts of exporting water through Jones and Banks pumping plants. Record exports and pelagic habitat degradation continue.
  • Provide pulse flows of approximately 17,000 cfs or higher as measured at Freeport periodically during the winter-run emigration season (i.e., December-April) to facilitate outmigration past Chipps Island. There are no late fall pulse protections or prescribed reservoir releases during the key periods that winter-run salmon emigrate through the Bay-Delta.3
  • Restore, improve and maintain salmonid rearing and migratory habitats in the Delta and Yolo Bypass to improve juvenile salmonid survival and promote population diversity. Lots of talk and little action over the past decade.
  • Minimize the frequency, magnitude, and duration of reverse flows in Old and Middle River to reduce the likelihood that fish will be diverted from the San Joaquin or Sacramento rivers into the southern or central Delta. Limited restriction in export-induced reverse flows with limited benefit; plans to allow higher levels of exports.
  • Continue to evaluate head of Old River barrier operations to identify and then implement the best alternative for maximizing survival of juvenile steelhead and spring-run Chinook salmon emigrating from the San Joaquin River. Evaluation continues with no implementation.
  • Modify Delta Cross Channel gate operations and evaluate methods to control access to Georgiana Slough and other migration routes into the Interior Delta to reduce diversion of listed juvenile fish from the Sacramento River and the San Joaquin River into the southern or central Delta. No progress.  Gates remain open in winter-run emigration season (Nov-Dec).  No resolution of Georgiana Slough problem.
  • Through additional releases in the San Joaquin River system, augment flows in the southern Delta and curtail exports during critical migration periods (April-May), consistent with a ratio or similar approach. Continuing conflict and lack of resolution.
  • Design and implement a project(s) to: (1) allow adult salmonids (and sturgeon) from the Sacramento Deep Water Ship Channel (SDWSC) to pass the channel gates and enter the Sacramento River (or block adult salmonids from entering the SDWSC); and (2) minimize fish passage from the Sacramento River into the SDWSC. No progress.
  • Establish Vernalis flow criteria that incorporate the flow schedules of the San Joaquin River and tributaries in order to increase juvenile salmonid outmigration survival. Continuing conflict and lack of resolution.
  • Evaluate whether predator control actions (e.g., fishery management or directed removal programs) can be effective at minimizing predation on juvenile salmon and steelhead in the Delta. Continuing evaluation and minimal resolution.
  • Develop and implement a program to reintroduce winter-run Chinook salmon, spring-run Chinook salmon, and steelhead to historic habitats upstream of Shasta Dam. The program should include feasibility studies, habitat evaluations, fish passage design studies, and a pilot reintroduction phase prior to implementation of the long-term reintroduction program. Minimal progress and no implementation.
  • Restore and maintain riparian and floodplain ecosystems along both banks of the Sacramento River to provide a diversity of habitat types including riparian forest, gravel bars and bare cut banks, shady vegetated banks, side channels, and sheltered wetlands, such as sloughs and oxbow lakes following the guidance of the Sacramento River Conservation Area Handbook (Resources Agency of the State of California 2003). Minimal progress and lack of funding and interest.
  • Develop and implement a river flow management plan for the Sacramento River downstream of Shasta and Keswick dams that considers the effects of climate change and balances beneficial uses with the flow and water temperature needs of winter-run Chinook salmon, spring-run Chinook salmon, and steelhead. The flow management plan should consider the importance of instream flows as well as the need for floodplain inundation.  No progress, further degradation.
  • Avoid full power peaking at Trinity and Carr Power plants during sensitive periods for water temperatures to reduce water temperatures in the Sacramento River. Evaluate impacts of power peaking operations in the Trinity River, Sacramento River and Clear Creek.  No progress and lack of action.
  • Providing and/or improving fish passage through the Yolo Bypass and Sutter Bypass allowing for improved adult salmonid re-entry into the Sacramento River (long-term). Limited progress and lack of implementation.
  • Implement studies designed to quantify the amount of predation on winter-run Chinook salmon, spring-run Chinook salmon, and steelhead by non-native species in the Sacramento River. If the studies identify predator species and/or locations contributing to low salmonid survival, then evaluate whether predator control actions (e.g., fishery management or directed removal programs) can be effective at minimizing predation on juvenile salmon and steelhead in the Sacramento River; continue implementation if effective.  No progress.

In conclusion, the extension of water rights permits and the update of water quality control plans offer opportunities to incorporate all of the above and other Recovery Plan actions that would lead toward Central Valley salmon and steelhead recovery.  These processes should not proceed or be approved without comprehensive acknowledgement and incorporation of recovery actions.

Winter Pulsed Flows for Fall Run Salmon

There has been a series of storms in the Central Valley in early winter 2019 that have stimulated the migration of salmon fry and smolts in the lower Sacramento River toward the Bay-Delta (Figure 1). However, these storms have not created flow pulses in the 25 miles of prime spawning habitat in the Sacramento River directly downstream of Keswick Dam (River Mile 300) (Figures 2 and 3). High flows at Bend Bridge (RM 250) have originated from largely un-dammed Cow, Cottonwood, and Battle creeks. Although inflow to Shasta and Keswick reservoirs has exceeded 50,000 cfs during two recent storm events (Figure 4), these reservoirs are releasing only a few thousand cfs.

Based on the Red Bluff screw trap catch (top chart in Figure 1), there are likely many wild fry in the upper river directly downstream of Keswick Dam that could take advantage of flow pulses to start their 300–mile journey toward the San Francisco Bay-Delta and its optimal fry rearing habitat. Flow pulses of 3000-5000 cfs during storm events added to the existing Keswick release could go a long way toward increasing the production of wild fall-run Chinook salmon.

Figure 1. Screw trap collections of fry fall-run salmon at Red Bluff (RM 240) and Tisdale Weir (RM 120) August 2018 to mid-January 2019.

Figure 2. Sacramento River flow at Keswick Dam (RM 300) (red line) and Bend Bridge (RM 250) (green line) 10/1/18-1/16/19.

Figure 3. Map of upper 100 miles of Sacramento River downstream of Keswick Dam with approximate percent of salmon spawning by sub-reach. (CDFW data)

Figure 4. Inflow to Shasta Reservoir in January 2019.

Response to Bay-Delta Science Paper on The Problems with Coleman Hatchery Salmon Straying

In a Maven 1/17/19 post, US Fish and Wildlife Service hatchery managers discuss problems that have developed from trucking salmon smolts from the Coleman National Fish Hatchery (Coleman NFH) to San Francisco Bay. Chief among these problems is that juvenile fish trucked from Coleman NFH stray into other Central Valley rivers as spawning adults, rather than returning to Coleman NFH. This has become a general argument for releasing Coleman NFH smolts near Redding instead of trucking or barging them to the Bay.

During the 2013-2015 drought, many Coleman NFH smolts were trucked to the Bay for release to meet the hatchery’s goals:

The management goals for the hatchery are to provide about 1% of their production or about 120,000 fish from each brood year to the ocean fishery, the freshwater sport fishery, and returns to Battle Creek for brood stock, all while trying to reduce negative impacts on naturally spawning fish.

From 2013-2015, 35.5 million fall run smolts, about 12 million per year, were reared for release by the Coleman NFH. In 2013, all were released at the hatchery into Battle Creek. In 2014, 3.4 million were released at the hatchery, and the remainder were trucked to the Bay. In 2015, all 12 million were trucked to the Bay. Since 2015, all Coleman NFH fall-run smolts have been released at the hatchery.

Trucking during the drought did meet the 1% production goal, but did not provide adequate hatchery returns for broodstock and did not achieve low straying rates.1 The USFWS has since chosen to ignore the production goal in order to achieve the other two goals. In dry years, the 12 million smolts now provide 10,000-20,000 adults (0.1-0.2%) to fisheries instead of 100,000-200,000 (1-2%). Instead of increasing hatchery production by barging smolts or improving post-release river conditions (higher flows), the fall-run salmon production program at Coleman NFH, designed explicitly as mitigation for loss of salmon from the federal Central Valley Project, is not meeting its primary mitigation goal.

In the response to Maven’s questions on USFWS presentation at the Bay-Delta Science Conference, the USFWS managers offered the following responses:

Is Straying Bad?

  • This occurs because fish that do not naturally emigrate through the river system lose the opportunity to imprint properly and may be unable to locate their natal area when they are ready to spawn. Response: High stray rates are unique to the federal Battle Creek Coleman NFH, partially because many of their returning adults spawn in the upper Sacramento River (as intended) and do not move into Battle Creek, and are thus considered strays. Regardless of imprinting influence, returning adults to the Sacramento River are confronted with poor flows and high water temperatures above the mouth of the Feather-Yuba-Butte Creek, Mokelumne, and American rivers, so they choose those rivers out of necessity. This problem does not occur at the Feather, American, and Mokelumne state hatcheries. These other hatcheries have also transported stray, earlier-returning Battle Creek adults (or fertilized eggs) to the Coleman Hatchery to help Coleman offset its egg shortages.
  • Hatchery fish that stray into natural spawning areas can detrimentally affect natural fish populations through genetic, ecological, and behavioral mechanisms…. Increased straying by hatchery fish may reduce genetic diversity within and among salmon populations. Response: While this is generally true for pristine natural salmon watersheds, this concern was long ago lost in the Central Valley after a century of disturbance and hatchery interference. Eggs have been shared, even from out of state, and even from different runs (hatcheries and dams have forced mixing of spring-run and fall-run spawners). Hatchery strays continue to dominate runs in non-hatchery rivers; without the strays, there would be few if any salmon in these rivers. Straying is also a natural process needed to retain population fitness, resilience, and genetic diversity.
  • Likely due to the prevalence of off-site release practices at Central Valley hatcheries, Central Valley fall Chinook Salmon have lost locally adapted genes and become one large, genetically homogeneous population (see Johnson et al 2012). Response: Adapted genes were lost decades ago before off-site releases. Johnson et al were describing how hatchery dominance covers up underlying problems in wild populations, not necessarily how it causes the underlying problems. This is a real concern in the Central Valley where only 25% of the fall run hatchery smolts are marked. The true wild components of individual river runs need protection. For some rivers, natural spawning areas can be reserved for true wild spawners (e.g., Battle Creek, Yuba River, Mokelumne, Calaveras, Butte Creek, etc.). Wild spawners can also be relocated above rim dams. Conservation hatcheries can use “wild” spawners.
  • Furthermore, salmon that are spawned and reared in fish hatcheries may become quickly adapted for characteristics that favor their survival and reproductive success in the hatchery environment while, at the same time, diminishing their ability to survive and reproduce in the natural environment. Response: while potentially (and historically) true, modern hatchery programs minimize or should minimize, if not reverse, these tendencies.
  • Stray hatchery fish may also compete with natural fish populations for limited resources, including competition for preferred spawning areas by adults and competition for food resources and habitat by juvenile fish. Response: Again, while generally and historically true, hatchery adult returns now take the place of wild adults in increasingly depressed amounts of spawning habitat in Central Valley rivers. Also, it is generally known that in many cases wild adults out-compete hatchery adults for habitat. Also, in most Central Valley rivers, hatchery fall-run adults can be effectively excluded from primary spawning areas. Hatchery smolts can readily be excluded from natural rearing areas by controlling timing and location of releases. In arguing against barging or trucking, USFWS managers are in essence arguing to continue releasing their hatchery smolts into prime natural rearing areas.
  • When hatchery fall Chinook Salmon from Coleman NFH stray at high rates, the freshwater fishery may be redistributed to other parts of the Central Valley and sport fishing in the upper Sacramento River fishery is negatively impacted. Response: Low flows and high water temperatures are the biggest contributor to poor upper Sacramento River salmon fishing.2 Also, Coleman hatchery adults that spawn in the upper Sacramento River or that are caught by sport fisherman in the Sacramento River upstream of Battle Creek are considered strays, even though they are produced to mitigate for Shasta Dam.
  • High stray rates of trucked hatchery fish may impact the ability of Coleman NFH to meet its annual fish production targets. For example, in 2017 (which corresponded to age-3 adult returns of fish that were 100% trucked), less than 350 adult salmon returned to the hatchery. At a minimum, Coleman NFH needs to spawn 2,600 pairs of adult salmon to meet the production target of 12 million juveniles. As a result, Coleman NFH released less than 6 million juveniles in the spring of 2018, which will result in fewer fish available to achieve our management goals in future years. Response: Then why not release a portion of the smolts in the Bay as for brood year 2013 (2014 releases)? Other potential measures to increase egg take outlined by the authors can also be enhanced.

Need for Trucking

  • California’s drought had some negative impacts for Coleman National Fish Hatchery….The one percent contribution goal to the fisheries and returns to Battle Creek was not able to be achieved under the drought conditions. Response: The drought was not to blame. Reclamation’s water right permits require measures to protect salmon, even during droughts. During the 2013-2015 drought, Reclamation delivered too much water to Sacramento River settlement contractors. This left Reclamation too little water to meet the conditions in its water rights permits that are designed to protect salmon. Water management during droughts is the problem.
  • Despite our extra efforts to collect additional eggs, we only met about half of our production target. We’ve undertaken a study to assess fish survival under different release strategies. This information will hopefully allow for adaptive management, based on changing environmental conditions and may give us some flexibility to release fish onsite to meet our multiple management goals in the future. Response: If Reclamation provides environmental flows from Shasta, and if USFWS times releases of hatchery juveniles at Coleman NFH to water conditions, then Battle Creek releases may produce more adult salmon. Some amount of trucking may be necessary to meet overall mitigation goals.


Hatchery program managers should not give up on trucking and on reducing high stray rates. They should consider barging juvenile salmon to better imprint smolts and improve smolt survival. Federal water managers also need to improve lower Sacramento River conditions for returning adults, in order to reduce straying. Water contractors and state/federal purveyors must also collectively limit their water diversions to meet water right permit conditions and water quality standards that are designed to protect fish. Egg taking should be increased if hatchery releases are to continue, in order to meet mitigation goals. These measures will all help hatchery managers meet their adult production goals and mitigation commitments. Trucking, a standard practice at state hatcheries in all year types, may be necessary, especially in periods of drought, to meet mitigation goals.