Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Butte Creek Spring Run Salmon – Status End-of-Year 2020

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When I last reported in May 2017 on the status of Butte Creek spring-run Chinook salmon, the population had hit lows as a consequence of the 2013-2015 drought.  I am happy to report the run’s rebound after the drought with new reported and revised CDFW escapement estimates.

Following escapement in 2017 that was the lowest since 1998, the population estimate increased to 6253 in 2019 (Figure 1).  The spawner-recruit relationship (Figure 2) continues to indicate a positive spawner-recruit relationship, with and positive responses to normal water year 2016 in the 2018 run and to wet water year 2017 in the 2019 run.  Though 2018 was a below-normal water year like 2016, the run in 2020 produced by 2018 water conditions has been characterized as small.1 A small 2020 run may be the consequence of the low number of 2017 spawners.  In addition, the devastating 2018 Camp fire in the watershed may have adversely affected the 2020 adult returns and future spawning runs.  But overall, the outlook for the 2021 and 2022 runs is promising given the improved number of spawners in 2018 and 2019.

Figure 1. Butte Creek spring-run salmon escapement estimates, 1975-2019.

Figure 2. Spawner-recruit relationship of spring-run Chinook salmon for Butte Creek. Numbers shown represent recruits (number of returning adults) for year displayed. The color of the number shows the conditions two years previously, when young reared in Butte Creek and then emigrated to the ocean. A red number shows a dry year rearing and emigrating conditions. Blue designates wet year rearing and emigrating conditions. Green designates normal year rearing and emigrating conditions. For example, 17 represents escapement in 2017, while its red color designates drought conditions in 2015.

Tuolumne River Salmon Runs in Decline – End-of-Year 2020 Status

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After decades of dominating the overall salmon run in the San Joaquin River watershed, the salmon run in the Tuolumne River now lags behind the runs in her sister rivers.  The Tuolumne River is a San Joaquin River tributary with no hatchery.  Its salmon runs are declining (Figure 1).  Unlike her sister rivers the Stanislaus and the Merced, the Tuolumne salmon run did not rebound as well after the 1987-1992, 2007-2009, and 2013-2015 droughts (Figure 2).

The Tuolumne run has had difficulty recovering from droughts because spawner numbers in subsequent years are too low.  There is a positive spawner-recruit relationship, heavily influenced by water year conditions (Figure 3).  Recruitment (run size) is influenced by the number of parent spawners (three years earlier), poor rearing year conditions (two years earlier), and poor conditions in the year adults return.. Runs from 1990-1992 had all three of these adverse conditions, which led to a 99% loss of their potential (two log levels).  The third years of the two recent droughts (2009 and 2015) had similar reduced potential, though with only two of the adverse conditions (poor rearing conditions and poor adult returns).

In a recent post, I related near-record-low salmon runs over the past several years in the Yuba River, a Sacramento River tributary that is similar to the Tuolumne in that it has no hatchery.  Like the Yuba, the Tuolumne salmon run is also markedly influenced by hatchery strays from other Central Valley rivers.  Hatchery strays from other rivers (Figure 4) dominate otherwise poor runs in the Tuolumne River in the years following droughts.  Many Battle Creek and Mokelumne River hatchery smolts trucked to the Bay in 2014-15 later strayed to the Tuolumne River to spawn.

Lack of returning wild salmon that are of Tuolumne River origin, and the dominance of hatchery strays after droughts, do not bode well for the native Tuolumne salmon run.  Resource agencies and other science experts have recommended maintaining a run of at least 500 native spawners for the run to remain “viable” (McClain 2010).  While recent runs since the 2013-15 drought have averaged near 1000 spawners, the fact that 60-70% are hatchery strays indicates that this goal has not been met over the past 15 years.  To increase wild salmon production, the State Water Board needs to adjust the allocation of Tuolumne River water, a process the State Water Board began in 2018.  Changes in the operation of the Delta pumps to reduce pumping during the emigration season would improve the success of all San Joaquin watershed salmon runs.  As native populations improve, river managers could reduce the influence of hatchery strays by ‘sorting out’ strays at the adult counting weir in the lower Tuolumne River; however, this would necessitate marking all Central Valley hatchery smolts.

Figure 1. Fall run Chinook escapement to the Tuolumne River 1975-2019. Data Source.

Figure 2. Fall-Run Chinook salmon escapement in San Joaquin River tributaries 1975-2019. Data Source.

Figure 3. Spawner-recruit relationship for Tuolumne River fall-run Chinook salmon. Numbers are log transformed minus 1 (2.00 = 1000). Numbers are recruits in their spawning return year. Red number is dry water year two years earlier when rearing as young. Red circle is dry year adult return year. Blue is wet year. Green is normal water year.

Figure 4. Source of hatchery strays in Tuolumne River spawning ground surveys in 2016 and 2017. Note only 25% of hatchery smolts are marked. Source.

Winter Pulsed Flow for Salmon Needed Now!

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Winter pulse flows benefit fall-run salmon fry by helping them emigrate to the Delta and Bay nursery areas (see discussion in February 2019 post). The tailwater spawning reaches of dams need reservoir releases to stimulate emigration of fry (Figure 1). Such releases piggy-back on stormwater flows in downstream tributaries, such as those in late January 2021 (Figure 2).

Nearly all Central Valley reservoirs are capturing recent high precipitation from their upper watersheds. With forecasts of further substantial rainfall into mid-February 2021, modest reservoir releases would provide substantial potential benefits to Central Valley salmon populations.

Figure 1. Sacramento River fall-run salmon fry catch near Red Bluff (river-mile 240) in winter 2020. Note that flow pulses stimulated winter fry emigration.

Figure 2. Flows from Shasta/Keswick reservoirs (river-mile 300, brown) and at downstream sites Bend Bridge (river-mile 250, green) and Wilkins Slough (river-mile 125, blue) in winter 2021. Note that tributary inflows created flow pulses in lower reaches of the Sacramento River.

Central Valley Steelhead 2021

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The Delta Science Program plans to host a Steelhead Workshop on February 17 – 19, 2021.  The purpose of the workshop is to “identify challenges to managing and monitoring Central Valley steelhead with the goal of identifying collaborations that are needed to improve the monitoring and science network for the species in the San Joaquin basin.”  While commendable and needed, such a workshop could and should cover the entire Central Valley Evolutionary Significant Unit (ESU), all of which must pass through the Delta on the way to and from the Pacific Ocean.

Although Central Valley steelhead science and management can succinctly be described as a mess, there are a few basic facts and misconceptions worthy of note that are useful in considering steelhead management in the Central Valley.

First, the facts:

  1. Steelhead are rainbow trout that have the genetic inclination to spend some of their life cycle in the ocean. Most rainbow trout have such an inclination, but some populations have long ago given up on that inclination (g., redband rainbow trout).

  2. In the Central Valley, all rainbow trout residing in anadromous waters are considered steelhead and are thus protected unless their adipose fins are clipped, which definitively shows hatchery origin.

  3. Rainbow trout of a wide range of origin, stocked or wild, live in or above dams in the Valley and are not designated steelhead. Some are remnants of steelhead trapped behind dams.  Other were hatchery raised or perhaps are remnants of long-ago geologically isolated populations.  Many of these non-steelhead pass over or through the dams and mix with steelhead, essentially becoming steelhead and influencing steelhead population genetics.

  4. All steelhead populations in the Valley have some degree of domestication from more than 100 years of hatchery influence and manipulation. Hatcheries (federal, state, and private) continue to influence population genetics.  Valley hatcheries have brought in eggs from many sources (g., Columbia River, coastal stocks, interior stocks such as Kamloops rainbow trout).  Hatcheries manipulated many important natural traits through selective breeding (e.g., run timing, age of maturity, growth rate).  Such changes affected the genetic integrity of locally adapted populations, adapted traits gained over thousands of generations.  Some hatchery sources were selected for traits better suited for hatchery managers or anglers than for natural diversity and population endurance.

  5. Valley steelhead come in many different breeds and colors, with distinct characteristics, traits, behaviors, and appearance. The basic breeds are often described by run timing:  winter, spring, summer, and fall, although most spawn in winter or spring.  Some examples are shown in attached figures below.

  6. Natural selection continues to adjust to human influences, albeit in competition with hatchery domestication.

Some misconceptions:

  1. Hatcheries are managed for benefit of natural, wild, or native steelhead populations. No. Hatcheries are managed to meet mitigation smolt production quotas at minimal cost, with some consideration for angler preferences (e.g., trophy size).  Hatchery domestication effects on genetic integrity are severe and not lessening.

  2. Central Valley steelhead are not in danger of extinction. Wrong.  They are in danger, which is why they are state and federally listed, and why no wild (unmarked) rainbow trout can be harvested in the anadromous zone of the Central Valley.  Wild “native stocks” are rare and declining.

  3. Spawning and rearing habitat in rivers and dam tailwaters are maintained to protect wild steelhead.   Protective standards are inadequate or often unmet.  Natural spawning and rearing habitats are degraded and are further deteriorating or being lost.  Flows are too low, and water temperatures too high.

  4. Steelhead are compatible with introduced non-native sportfish. No.  Striped bass, black bass, catfish, sunfish, and American shad all prey upon steelhead – the total population effect is substantial.  Since predatory fish cannot be eradicated, the interaction between steelhead and predators needs to be managed.

  5. Climate change is the cause of declining natural populations. Though climate change is real and exacerbates harmful conditions for steelhead, blaming climate change for the decline of steelhead is just a convenient excuse.

Management needs:

  1. Improved monitoring of steelhead population dynamics is needed. Despite the angler-funded steelhead stamp program, there is minimal monitoring of adult spawners or juvenile  Screw traps are for migrating fry, but steelhead fry don’t migrate like salmon.

  2. River habitats should be restored and improved. Rivers should not be treated just as conduits from hatcheries to the ocean.  Steelhead over-summer at least one year before emigrating to the ocean.

  3. Mitigation hatcheries should be converted to conservation hatcheries. The hatchery programs need a cleansing.  Also, hatchery rainbows released above dams should be marked.

  4. Spawning habitat should be for wild, native steelhead. Steelhead sanctuaries are needed.  Every effort should be made (selective barriers) to limit access to these areas by hatchery or stray steelhead, and by migratory non-native predators and competitors such as shad and stripers.

  5. Flows are needed to increase survival of wild steelhead fry and smolts. Steelhead are genetically adapted to emigrate with the natural flow pulses of fall, winter, and spring.  Reservoirs have eliminated or reduced such flows.  Without the flows, smolts won’t migrate or survive the predator gauntlet.  Trap and hauling wild smolts around the lower river and Delta predator gauntlet is an option for dry years.

  6. Flows are needed to improve attraction of adult migrants to spawning rivers. Again, steelhead need the flow pulses.

For more on steelhead see:

Native rainbow-steelhead from the lower Yuba River. Many wild rainbow trout do not migrate, choosing to remain in the cold tailwaters of dams, where they sustain high-quality sport fisheries.

An early fall run hatchery steelhead from the lower American River in October. Battle Creek hatchery steelhead smolts were stocked in the American River for one year to determine if they would be a viable more-native alternative to the American hatchery’s coastal Eel River origin stock. They were fine sport, susceptible to dry flies.

The American River hatchery program uses coastal origin stock that spawn in winter. Many spawners enter the river in late fall when fishing is closed to protect spawning salmon. Fishing is open in winter spawning season. This female caught in January was likely actively spawning. Native steelhead are spring spawners.

Longfin Smelt – 2020

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In a February 2020 post on the status of longfin smelt, I lamented the poor 2019 population index (Figure 1) and thus made a grim prediction for the future of the Bay-Delta sub-population of this state-listed endangered species.  The index in wet year 2019 should have been 10 times higher (one higher in log number).  Preliminary survey results suggest that the 2020 population index for longfin smelt will likely be as poor as those in 2018 and 2019.

In Figure 1 below, the 2020 index will likely show as a red 20 just above the red 14.  Most of the 2020 spawners came from the 2018 spawners (green 18 in Figure 1).  Like the 2018 spawn, the 2020 year class grew up in a drier year, upstream in Suisun Bay and the western Delta (Figure 2), as compared to a more western Bay distribution like wet year 2019 (Figure 3).

I am very concerned what will happen if winter 2021 stays dry and there are thus two dry water years in a row (2020 and 2021).  This would drive the 2021 production index down to 2015-16 levels.  Coupled with the absence of Fall-X2 flows in 2020 and the unusually low 2019 longfin index, a second straight dry year presents a serious threat to the population index in 2021 and future years.

Figure 2. Longfin smelt catch distribution in 2020 Survey 1 of 20-mm Survey. Delta outflow was 8,000-20,000 cfs. Source.

Figure 3. Longfin smelt catch distribution in 2019 Survey 1 of 20-mm Survey. Delta outflow was 160,000-180,000 cfs. Source.