Winter-Run Salmon Update – August 2020

In my last update, March 2019, I summarized the population trends of winter-run Chinook salmon through 2017. In this post I include run estimates for 2018 and 2019. The trend indicates the population is recovering from the poor runs in 2016 and 2017 (Figures 1and 2), which were the consequence of poor spawning and rearing conditions.

The improvement is the result of more hatchery contributions and better natural contributions. The strong spawner-recruit relationship continues (Figure 3), with an improved 2019 run that spawned (in hatchery and wild) in summer of normal year 2016 and reared and emigrated during wet water year 2017. In contrast, the poor 2016 and 2017 runs were a consequence of critical drought conditions during spawning (2013 and 2014) and rearing/emigration (fall-winter of water years 2014 and 2015). The 2017 run could have been even worse had hatchery smolt releases not been doubled in winter 2015.

NMFS (2019) concluded the recovery was due to increased hatchery contributions and “better water management”. The latter is simply not true. Year 2017 was a wet year that contributed to good fall-winter survival of broodyear 2016 (Figure 4). By December 2019 NMFS knew that its draft biological opinion was being revised to limit protections.1

The prognosis for the 2020 run (from brood year 2017) is good given wet year summer spawning and incubation conditions in 2017 and normal year winter 2018 conditions. With hatchery stocking back to the normal 200,000 annual smolt level in the Sacramento River at Redding, a run of 3000-5000 can reasonably be expected despite the depleted spawning run in 2017. High summer egg-to-fry survival in 2017 (Figure 4) will also contribute. The 2020 run may also benefit from the initial release of 215,000 winter run hatchery smolts into Battle Creek in 2018. Some of these will return as two-year-old “jacks and jills” in 2020.

Several factors make the prognoses for the 2021 and 2022 (and future) runs less optimistic. Egg/fry survival of wild winter-run was lower again in 2018 and 2019 (Figure 4). The new (October 2019) federal Biological Opinion for winter-run is less protective than the Opinion it replaced,2 and the Bureau of Reclamation’s new water management is explicitly directed toward maximizing water deliveries.

On the positive side, hatchery releases including releases into Battle Creek continued in 2019 and 2020, and the estimates of migrating juvenile winter-run were higher for brood year 2019 in wet summer 2019 (Figure 5). As a result of a Settlement Agreement with CSPA, the State Water Board has required the Bureau of Reclamation to develop new protocols to meet water temperature requirements in the Sacramento River. It remains to be seen how these protocols translate into practice.

In the past three decades, the essential needs for winter-run salmon have not been met.3 Management of winter-run salmon must improve survival of wild eggs and juveniles in the summer spawning and fall-winter rearing-emigration seasons, with supplementary hatchery smolt releases as necessary. We cannot simply rely on wet years to keep wild winter-run salmon going in the Sacramento River.

Figure 1. Spawning population estimates of adult winter-run salmon in the upper Sacramento River from 1974 to 2019. Source: CDFW GrandTab and NMFS.

Figure 2. Spawning population estimate since 1997 showing proportion of hatchery and wild adult spawners. Source: NMFS (2019).

Figure 3. Spawners versus recruits (spawners three years later) transformed (logx minus 2). Year is recruit year spawners. For example, 2017 is the run size for 2017, representing spawners from brood year 2014. Color denotes water-year type in fall-winter rearing/emigration year: bold red is critical year, non-bold red is dry year, yellow is below-normal year, and blue is wet year. For example, red 15 and dot margin represent critical water year 2013. Yellow dot fill represents spawning year was a below-normal water year. Note 2016 and 2017 had both critically dry year summer spawning and fall-winter rearing-emigration. The blue 2019 point is a preliminary estimate.

Figure 4. First summer survival rate by brood year based on egg and fry production rate estimates. Egg number is derived from adult spawner estimates. Fry number is derived from Red Bluff screw trap estimates. Source: NMFS.

Figure 5. Brood year winter-run salmon early life history and abundance (2005-2019) as measured at Red Bluff. Source:


Partnership Shares Science to Find Fish and Water Solutions

“This month six California and federal agencies representing water management, fish, and wildlife, along with the Sacramento River Settlement Contractors, signed onto the Sacramento River Science Partnership. The Partnership establishes an interagency science collaborative in which members will develop, share and discuss science to inform water management activities and protection of fish in the mainstem Sacramento River.” (8/25/20 News Release)

  •  The seven signatories will foster and advance science to inform sustainable solutions to water management challenges including conflicts between water supply delivery and fish survival.

The time when anyone thought that the problems confronting Central Valley salmon could be solved with more science is long gone. The problems and solutions have not really changed in the 40+ years I have been involved. And the problems are only getting worse. Why is it so hard to address them?

The Problems

As a consequence of rainfall, snowmelt, reservoir storage and release, and water diversions, flows in the Sacramento River, have become so low and erratic that they strand salmon spawning redds and create prolonged high water temperatures in the juvenile rearing and migration reaches of salmon. It is a wonder that there are any wild salmon left. Without hatcheries, there would be few if any salmon in the Central Valley at all.

Spring-Summer Water Temperatures

Spring-summer water temperatures in the lower Sacramento River are bad. They kill salmon and sturgeon, block migrations, lead to poor juvenile salmon growth, early migration, high predation, and cause huge predation problems for young hatchery and wild salmon. The high temperatures exceed state water quality standards and water project permit requirements. Yes, water temperatures were bad during the 2013-2015 critical drought, as might be expected (Figure 1). But they have also been bad in the five normal and wet years (2016-2020) since the drought (Figure 2). The safe level is 65°F, but the standard is set at 68°F, above which stress and higher mortality occurs. 68° is supposed to be an upper limit that should not be exceeded, and in past decades it rarely was. It is now the accepted norm, and even then it is not enforced.

In 2020 (Figure 3) spring water temperatures were detrimental to the upstream migration of endangered winter-run and spring-run salmon, emigrating juvenile fall-run salmon, and larval and juvenile sturgeon. High summer temperatures hinder migration of adult fall-run salmon and are detrimental to survival of winter-run fry, over-summering late-fall-run and fall-run salmon smolts, and rearing juvenile sturgeon.

Fall Drops in Water Levels

Often, usually in October-November, flow releases from Shasta reservoir drop sharply in response to decreasing downstream irrigation demands. The decreases lead to fall-run salmon redd dewatering in the upper river spawning area near Redding and poor habitat and emigration flows for winter-run and late-fall run juvenile salmon.


Adult and juvenile salmon are stranded throughout the Sacramento River floodplain after winter-spring, high-flow events. In addition, drops in water surface elevation of four feet in the fall (Figures 4 and 5), soon after spawning de-water the vast majority of fall-run spawning redds in the 20-mile spawning reach downstream of Keswick Dam. Drops in flows after floodway weir spills (Figures 6 and 7) strand adult salmon and sturgeon that are migrating upstream, and also strand juvenile downstream emigrants in the Sutter and Yolo floodway bypasses.

Hatchery Releases

Releases of millions of hatchery-raised salmon and steelhead smolts in winter and spring into the lower Sacramento River from federal and state hatcheries compromise wild salmon and steelhead fry, fingerling, and smolt survival throughout the lower Sacramento River. Hatchery salmon and steelhead prey upon and compete with wild salmon and steelhead, and attract non-native predatory striped bass that also feed on wild salmon and steelhead.


A new science plan for the upper reaches of the lower Sacramento River is not going to solve the problems that stem from failure to act on what science has told us for decades.

Solutions to the problems outlined above abound. These solutions are well documented in the Central Valley Salmon and Steelhead Recovery Plan (NMFS 2014) and other stakeholder plans.1 The most important solution, is water temperature limits in the lower Sacramento River, which were adopted decades ago in state water permits and water quality control plans. These limits designed to protect salmon are simply no longer enforced.

Figure 1. Water temperature in the lower Sacramento River from 2013-2015 critical drought years near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 2. Water temperature in the lower Sacramento River from 2016-2020 post-drought years near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 3. Water temperature in the lower Sacramento River in 2020 near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 4. Sacramento River flows in fall of 2013 below Keswick Dam near Redding.

Figure 5. Sacramento River water surface elevation in fall of 2013 below Keswick Dam.

Figure 6. Spills of water from Sacramento River over Tisdale flood control weir during the period from December 2013 to February 2015. Source: CDEC

Figure 7. Spills of water from Sacramento River over Tisdale flood control weir during the period from January 2016 to May 2017. Source: CDEC

Franks Tract Futures Project

The Franks Tract Futures Project is asking for additional comments on the State’s revised concept design.1 The project is an outgrowth of the State’s 2016 Delta Smelt Resilience Strategy, which recognized that Franks Tract is a death trap for state and federally listed Delta smelt.

The original design for the project included tide gates to keep salt and smelt from moving upstream from the western Delta into Franks Tract via the False River channel. Once in Franks Tract, the smelt would most assuredly not survive. A new design “transforms the project from an early focus on establishing habitat for the endangered Delta smelt to a project that has sought input from a broad range of stakeholders.” According to the project leader, Brett Milligan from University of California:

Balancing the project’s goals has been a challenge. The first round of this project, the feasibility study, met the water quality and ecology requirements but did not meet the recreational and local economy (requirements). We heard you loud and clear. More or less, this entire last year has been to try to bring in that third tier and to balance these and see if there’s a way that the project can meet all of these criteria and be beneficial to all. The original project design failed to earn public support after it was presented in January 2018. At a crossroads, the project managers made a critical decision. They scrapped the proposal and formed an advisory committee of stakeholders with varied interests in Franks Tract rather than try to force the initiative through the process, while fighting the public every step of the way.

The new design drops the barrier/gate option as “a non-starter,” Brett explained to me. But that was the essential element of the project – stopping salt (and smelt) intrusion into the interior Delta due to the pull of the south Delta export pumps. A temporary barrier has been installed in False River in drought years to protect Delta water supplies.

The conflict is over recreational access to Franks Tract from the west via False River. A similar barrier on Montezuma Slough further west in Suisun Marsh resolved a similar conflict with a boat passage lock that maintains boating access when the barrier is in use.

At this phase of design and permitting, it would seem wise to evaluate an alternative with the barrier that includes a similar boat passage facility, so that the affected public can understand the tradeoffs. That is the purpose of the environmental review process.

Saving Native Central Valley Salmonids

No, the fish below is not a Central Valley salmon or trout. It is a Yellowstone Cutthroat Trout from the Yellowstone River in Yellowstone National Park. This iconic species is beginning to recover from competition and predation by non-native brook, brown, rainbow, and lake trout. Yellowstone Park over the past decade has carried out an intensive eradication program of the non-native salmonids to save the iconic native cutthroat. A similar program has been underway to save the Snake River Cutthroat on the South Fork of the Snake River from Grand Teton Park in Wyoming downstream into Idaho. The eradication programs include rotenone poisoning of tributaries, gill-netting (lake trout in Yellowstone Lake), and regulations requiring angler removal (rainbow trout).

Yellowstone Cutthroat Trout caught and released in the Yellowstone River in Yellowstone National Park summer 2018

California has excellent programs to protect some of its iconic trout and salmon through strict regulations and habitat protection and enhancement.

  • Redband Rainbow Trout in the upper McCloud River
  • Golden Trout in the upper Kern River
  • Lahontan cutthroat of the Truckee drainage.
  • Coastal cutthroat (NorthCoast streams)
  • Paiute cutthroat of the eastern Sierras.
  • Winter Run Chinook salmon (endangered) spawning grounds upstream of Redding are now closed to trout angling.
  • Spring Run Chinook Salmon (threatened) spawning tribs protected
  • Wild steelhead – no harvest in mark-selected fisheries (photo below)

Wild Rainbow Trout/Steelhead caught and released in the lower Yuba River near Marysville January 2019.

One survival bottleneck that needs opening for salmon and steelhead in the Central Valley is predation by non-native fish. There is a long list of non-native and native predators from which native fish need protection. The best protection is to minimize native-nonnative habitat interactions. That can best come from adequate physical-geographical habitat and habitat water quality for natives while minimizing non-native fish habitat. Changes are necessary because of global warming and continually increasing demands on water. Stream flows are too low, water temperatures are too high, waters are clearer, and in-stream cover is low, factors that all favor non-native predators and competitors.

Because many of the non-natives are sportfish with strong angler followings, non-lethal controls best serve to reduce overall predation effects on native fishes.

  • Provide natural spring flow pulses in rivers and tributary tailwaters to help emigrating salmonids avoid predators.
  • Keep water temperatures lower in rearing habitat and migrating routes of native fish.
  • Maintain the low salinity zone, the primary rearing area for native fishes, in the Bay downstream of the Delta.

At some point population controls on non-native fish may have to be considered despite their inherent problems and low potential for success.1 Note that despite the use of 50 miles of gill nets and removal of hundreds of thousands of pounds of lake trout each year in Yellowstone Lake, lake trout remain abundant. Predator control through removal would be far more difficult in the Central Valley and Bay-Delta.

Summary and Conclusion

I remain skeptical on how effective the individual actions can be, but a comprehensive multi-action program such as that employed for the Yellowstone Cutthroat Trout has some chance of success. Such a program would come with tough choices and require considerable resources, but may need to be part of saving Central Valley salmon and steelhead. Focus should be on increasing the amount of native fish habitat and bettering spawning, rearing, and migratory habitat conditions.


Delta Smelt Sanctuary – Deepwater Ship Channel

In a March 2020 post, I described where the remnants of the endangered Delta smelt population spawn and rear in the Sacramento Deepwater Ship Channel (Ship Channel) in the north Delta (Figure 1). In this post, I describe how the rearing conditions in the Ship Channel are poor. This can be seen by comparing habitat conditions in the Ship Channel with those in the lower Sacramento River channel at Freeport several miles to the east in late spring 2020.

Net Flow

Net flow (cfs) in the Ship Channel remains near zero, since the gate at the north end of the channel near Sacramento remains stuck in the closed position as it has been for several decades (Figure 2).

Water Temperature

Water temperature (oC) is significantly higher in the stagnant flows of the Ship Channel than at Freeport, often reaching into the lethal range 23-25°C for Delta smelt (Figure 3).


Salinity (conductivity) is much higher in the Ship Channel because of discharges from urban sewage treatment plants and agricultural operations (Figure 4).


Turbidity is much higher in the Ship Channel due to higher plankton production and port-bound ship traffic in the relatively shallow and narrow Ship Channel (Figure 5).

Dissolved Oxygen

Dissolved oxygen levels are much lower in the Ship Channel because of warmer water, high concentrations of suspended organic sediments, and higher plankton production (Figure 6).

Interpretations and Conclusions

Delta smelt are attracted to the Sacramento Deepwater Ship Channel in winter and early spring to spawn in the relatively warm, low salinity, turbid, and more productive water. The adult smelt can also easily tidal-surf up the ship channel without having to content with strong downstream currents of the Sacramento River channel. Their eggs hatch early to an awaiting abundant plankton food supply. However, in spring the Ship Channel lacks net downstream flows to carry the young smelt to the Bay. By late spring, water temperatures in the Ship Channel reach lethal levels for the young smelt.

Opening the gate at the north end of the Ship Channel would help to alleviate the problems by providing net flow with cooler water temperatures, and by flushing and diluting the stagnant waste waters in the Ship Channel. An operable gate at the head of the Ship Channel would allow adaptive management of the habitat conditions for smelt.

Figure 1. Locations where Delta smelt young were captured in EDSM surveys in July 2019. Circles represent regions. Numbers are total July catch in region. The 94 represents the young smelt captured in the Deepwater Ship Channel.

Figure 2. Net daily flow (cfs) in the Ship Channel and in the Sacramento River at Freeport in June 2020. The green line shows flow in the Ship Channel.

Figure 3. Water temperature in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows the water temperature in the Ship Channel.

Figure 4. Conductivity (salinity) in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows salinity in the Ship Channel.

Figure 5. Turbidity in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows turbidity in the Ship Channel.

Figure 6. Dissolved oxygen in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows dissolved oxygen in the Ship Channel.