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.

Salmon and Steelhead Recovery Plan Series – Yuba River

Posted on January 7, 2025 by Tom Cannon

This is the second post in a series on California Salmon Recovery. I have chosen this post on the Yuba River salmon for the second in the series as an example of posts to come that summarize plans for each major salmon stream. Posts will also include summaries of a recommended hatchery program, fisheries harvest management, water supply and water quality management, wild salmon sanctuaries, and monitoring.

The Yuba River is the largest tributary of the Feather River, which in turn is the largest tributary of the Sacramento River. The Yuba River Watershed drains 1,339 square miles of the western slope of the Sierra Nevada and includes portions of Sierra, Placer, Yuba, and Nevada counties. The three branches of the Yuba River are the North Yuba, Middle Yuba, and South Yuba rivers (Figure 1).

Like many of the Sierra Nevada watersheds, the Yuba River has large dams and multipurpose water storage reservoirs. Major high-elevation reservoirs in the Middle Yuba and South Yuba drainages include Jackson Meadows and Bowman, owned by Nevada Irrigation District (NID), and Fordyce and Spaulding, owned by Pacific Gas and Electric Company (PG&E). These entities own multiple smaller reservoirs in the watershed at elevations above 4000 feet. Together, in a hydropower and water supply system that in part dates to the Gold Rush, NID and PG&E export an average of 400,000 acre-feet of water from the Yuba watershed to the adjacent Bear River watershed each year.

Legacy gold mining is also a source in the Yuba watershed of large volumes of alluvial sediment stored in river channels, bars, and floodplain terraces. Much sediment has been transported and deposited in New Bullards Bar and Englebright reservoirs, the watershed’s two largest low-elevation reservoirs, as well behind smaller dams (e.g., Our House Dam, Daguerre Point Dam) and the lower river floodplain (e.g., the Yuba Goldfields). These reservoirs and dams also block natural sediment transport processes that generally support spawning and rearing habitats of salmon.

The North Yuba River flows into New Bullards Bar Reservoir, constructed in 1970 and owned and operated by the Yuba Water Agency (YWA). The reservoir has a total storage capacity of 966 TAF and a minimum pool of 234 TAF. It is the principal storage facility of the YWA’s Yuba River Development Project, one of the largest hydropower projects in the state, and is also in the cornerstone of YWA’s water supply operation for Yuba County agriculture and water sales under the “Yuba Accord.” The lower North Yuba flows for approximately two miles below New Bullards Bar Dam, where it is joined by the Middle Yuba to form the “mainstem” Yuba River. Approximately six miles farther downstream, the North Yuba flows are impounded in New Bullards Bar Reservoir and later returned to the mainstem Yuba through releases at YWA’s Colgate powerhouse. The mainstem Yuba River flows approximately one mile from the New Colgate powerhouse before entering Englebright Reservoir. The South Yuba River enters Englebright Reservoir from the southeast, about a mile farther downstream. The 24 miles from Englebright Dam to the mouth on the Lower Feather River at Marysville are termed the “Lower Yuba” River (Figure 1).

Daguerre Point Dam, located 11 miles downstream of Englebright Dam and 11.5 miles upstream of from the Yuba River’s confluence with the Feather River, allows diversion of water into three large water supply canals of the Yuba Water Project. The canal intakes are poorly screened and thus allow the entrainment or predation of juvenile salmon migrating downstream. Two fish ladders are only partially successful in passing migrating salmon and steelhead past the dam. The ladders do not meet modern fish passage criteria.

Historically, spring-run salmon and steelhead were able to ascend into the Yuba’s three branches to about the 4,000 ft elevation. On the North Yuba, they ascended as far upstream as the reach between Downieville and Sierra City, about 20-30 miles upstream of New Bullards Bar Reservoir. They probably ascended only about a mile or so up the Middle Yuba because of a barrier cascade. On the South Yuba, they may have ascended to the mouth of Humbug Creek about 15 miles upstream of the main Yuba.¹ Since the construction of Englebright Dam by the US Army Corps of Engineers in 1941, salmon and steelhead have been confined to the lower 24 miles of the Yuba downstream of Englebright Dam.

The Yuba River historically supported large numbers of spring-run and fall-run salmon as well as steelhead, but those numbers have greatly declined as the result of dams, historical gold mining, gravel mining, water resource mismanagement, and government apathy. In this post, I summarize actions needed to bring about Yuba River salmon and steelhead recovery.

Today, the most numerous Yuba salmon are the fall-run Chinook salmon (Figure 2). The 2017 spawning escapement estimate was a record low. The 2018 and 2019 runs were not much better. The 2020-2023 runs were only slightly higher. The 2013-2015 and 2020-2022 droughts, and associated water management, were major factors in these poor escapement levels. During these drought conditions, there was little flow into and through the Bay-Delta estuary, resulting in low numbers of smolts reaching the ocean and poor survival of returning adults in spawning runs.

The Yuba River’s salmon and steelhead runs now suffer from recruitment failure – the lack of spawners and smolt production to sustain the populations of salmon and steelhead. The 2018 and 2019 runs were poor despite being the product of normal (2016) and wet (2017) water years, water year types that historically produced stronger recruitment. The cumulative effect of poor recruitment is low spawner numbers – below target levels needed to replace the population (see Figure 3).

Another major factor in the long-term decline in the Yuba fall-run salmon is the continuing and persistent dwindling numbers of wild spawners and the increase in hatchery strays that now make up more than 90% of the run. Strays from hatcheries and other rivers lead to the genetic erosion of the locally adapted Yuba River wild salmon population. This was the diagnosis of the decline of the overall Feather River watershed population by Willmes et al., 2018.

Other contributing factors in the decline of Yuba salmon include (1) low survival of young salmon and steelhead due to poor spawning and rearing habitat, and (2) stresses and impediments the fish encounter during both upstream and downstream migrations. Poor spawning habitat can result in poor pre-spawn survival and poor subsequent egg and fry survival. Rearing habitat factors include excessively warm water, low streamflow, lack of spawning gravels, lack of cover, insufficient food supplies, predation (especially downstream of Daguerre Dam), and loss at water diversions. Harvest of adults in commercial and sport fisheries also limits recruitment, though there is no in-river harvest of salmon allowed in the Yuba River itself. High water temperatures in the lower Yuba River in late summer and fall may also discourage adult salmon from choosing the Yuba in some very dry years. Habitat stresses downstream of the Yuba in the Sacramento River, Delta, and Bay also limit the survival of Yuba River salmon in their migration to and from the ocean.

The cumulative impact of all these factors eventually leads to recruitment failure – the present state of the Yuba River salmon populations. Hatchery strays sustain the Yuba River salmon and steelhead populations under present conditions.

Recommended Actions

Listed below is an array of short term (ST) and long term (LT) recommended actions to recover salmon and steelhead in the Yuba River.

Action ST-1: Establish a new fish monitoring station at Daguerre Point Dam to develop a genetic parentage-based tagging (PBT) database for Yuba River salmon and steelhead.

An immediate need is the means to identify, on an annual basis, the origins and numbers of adult salmon and steelhead currently returning to spawn in the Yuba River. This information would allow resource agencies to assess the present population status and composition of Yuba River salmon and steelhead populations.

Action ST-2: Segregate and enhance the population of wild spring-run Chinook salmon that spawns between Englebright and Daguerre Point dams.

Segregate spring-run from fall-run salmon by restricting fall-run to spawning below Daguerre Dam. Operate Daguerre Point Dam ladders to allow passage of only spring-run salmon (and steelhead). Establish a spring-run salmon sanctuary between Englebright and Daguerre Point dams.

Action ST-3: Improve Yuba River habitat conditions for salmon and steelhead spawning, rearing, adult immigration and holding, and the outmigration survival of fry/smolts.

Habitat improvements would include streamflow, water temperature, and physical habitat elements (substrate, channel and floodplain configuration, large wood debris, water quality, and riparian vegetation). This would apply to habitat above Daguerre Point Dam for spring-run salmon and steelhead, and below Daguerre Dam for fall-run salmon and steelhead.

Action ST-4: Begin planning for a conservation hatchery for spring-run Chinook salmon and steelhead.

Resource agencies may find the Yuba River numbers and/or genetic diversity of spring-run salmon and steelhead numbers so low that stock supplementation from a temporary conservation hatchery is needed. Use spring-run sourced from the Yuba River’s natural spawning population, from a hatchery, or from another nearby natural spawning population for broodstock. Release hatchery eggs/fry into the Yuba River upstream of Daguerre Point Dam, Englebright Dam, or New Bullards Bar Dam. In the short-term, undertake conservation hatchery actions at the Feather River Fish Hatchery complex.

Action ST-5: Modify the Daguerre Point Dam fish ladders to provide seasonal temporary capture/release of upstream-passing spring-run salmon and steelhead (for monitoring), and to exclude fall-run Chinook. Improve the fish passage performance of the Daguerre ladders to meet modern (NOAA and CDFW) standards.

Over the short term, use gravity-fed sources or pumps to improve the attraction flows at the ladder entrances (i.e., downstream exits). Such efforts may prove effective in the late spring period under low-flow regimes to ensure minimal stress or delays of adult migrant spring-run salmon and steelhead.

Action ST-6: Conduct trap-and-haul experimental studies for spring-run salmon and steelhead from Daguerre Point Dam to the upper Yuba upstream of Englebright and/or New Bullards Bar reservoirs, consistent with existing study plans, to assess the various aspects and feasibility of such efforts.

Action ST-7: Begin the process of updating the fish screens at the major diversions at Daguerre Point Dam so they meet NMFS and CDFW criteria for downstream-migrating juvenile salmon and steelhead.

Action ST-8: Begin the process of installing fish screens at presently unscreened small agricultural diversions downstream of Daguerre Point Dam, near Hallwood and further downstream.

Action LT-1: Design and build new fish passage facilities at (or near) Daguerre Point Dam, which may include:

New fish passage infrastructure in the form of upgrades to existing ladders or other passage types such as the fish bypass system currently under evaluation.
A segregation weir in which adult salmon and steelhead can be captured, held for processing, and selectively released to continue passage past the dam. Undesirable non-salmonids can be precluded from bypass use (blocked or in some cases removed or relocated).
Downstream fish passage collection facilities (may be part of separation weir) to collect, count, and process juvenile (and downstream-migrating adult steelhead) salmonids, and other migratory fish (i.e., sturgeon, lamprey, shad, pikeminnow, suckers, etc.). The facilities would include the ability to collect wild juvenile salmonids for transport to the Bay in drier years or seasons when their potential for survival would be otherwise minimal.
Fish holding and processing facilities associated with holding and processing fish collected at the segregation weir, including cold-water sources (g., well systems).
A conservation hatchery for spring-run salmon and steelhead that would include egg taking, hatching, rearing, and processing facilities.
Modern fish screens for water diversion facilities at Daguerre Point Dam.

Action LT-2: Conduct large-scale pilot fish trap-and-haul projects

Establish one or more spring-run salmon sanctuaries above Englebright Dam. Trap-and-haul spring-run salmon and steelhead adults upstream for release in the Yuba River upstream of New Colgate Powerhouse or in the North Yuba River upstream of New Bullards Bar Reservoir. Capture downstream-migrating juveniles produced from the adult spawners in a net-collector in the Yuba River near the head of Englebright Reservoir and/or in upper New Bullards Bar Reservoir or in the North Yuba River upstream. Transport juvenile fish to a location downstream of Englebright Dam or Daguerre Point Dam, or to the Bay, for release, or to a conservation hatchery for supplementary rearing and later release to the Bay.

Action LT-3: Conduct large-scale fish habitat improvement projects

Improve migrating, spawning, and rearing habitat in salmon sanctuaries upstream and downstream of dams.

Figure 2. Yuba River fall-run salmon escapement 1975-2023. (Data Source: CDFW Grandtab)

Figure 3. Spawner-Recruit relationship (log-log transformed) for Yuba River fall-run salmon population. Numbers are recruits (escapement that year). Spawners are recruits from three years earlier. Red bold numbers are years where recruitment was influenced by critical drought years (during their spawn, first year of rearing, and upon return as adult spawners). Smaller non-bold red numbers reflect years with at least two below-normal water years. Blue bold numbers are years strongly influence by series of wet years.

Fish Bulletin 179, p. 78. ↩

California Salmon Recovery – Series Introduction

Posted on December 16, 2024 by Tom Cannon

This Introduction is the first in a series of posts that summarize elements of my recommended plan for Central Valley salmon recovery. Central Valley salmon runs over the recent five decades have varied from a total near 100,000 to near a million spawners with an average of 200-300 thousand (Figure 1). About 90% of the salmon runs have been fall-run. Spring-run and winter-run salmon have declined and are listed under the state and federal endangered species acts. All four runs are supported by hatcheries that raise about 30 million juveniles per year for release to rivers, the Bay-Delta, and the coastal ocean. Each of the run types are made up predominantly of hatchery-produced salmon. A few small stocks are comprised mainly of wild salmon, while most runs have a small “wild” or natural-born component. Rebuilding wild salmon stocks while providing for historic levels of commercial and recreational salmon harvest is the dual program mission.

The total number of adult salmon produced in the populations includes escapement to the spawning rivers described above as well as adult salmon harvested in the ocean, Bay-Delta, and rivers, prior to the spawning runs. These estimates are of the human harvest (Figure 2) and do not include harvest by marine animals or illegal fishing. Human harvest rates over the past four decades have been 50-70% on average except in years when the fishery is restricted (2008-2010 and 2023 and 2024) (Figure 2). Government agencies often restrict harvest when the Sacramento Fall Run Index falls to near a target minimum of 122,000, a condition commonly referred to as “overfished.”

The goal of my recovery plan is to return total adult salmon escapement to near a million fish, with a further harvest of 500,000 adult fish. The harvest would focus on hatchery fish, while habitat improvements would focus on rebuilding wild, genetically pure populations and their critical habitat.

The primary tools of the proposed recovery program include hatcheries, wild salmon sanctuaries, improvements in water project management and infrastructure, habitat enhancements, and changes to fishery management. Hatchery programs would include “production” hatcheries to produce marked smolts for release for harvest and maintaining spawning populations in rivers that cannot sustain wild populations. “Conservation” hatcheries would support the protection, maintenance, and development of “wild,” “genetically-pure” populations.

The actions I propose are not radical or new: they have been included in many plans and program recommendations for decades. Many have been successfully implemented on a small scale in the Central Valley or in other large salmon watersheds of the Pacific Northwest and Alaska.

Figure 1. Total Central Valley Chinook salmon escapement by run type 1975-2023. (Source: Grandtab)

Figure 2. Sacramento River watershed salmon population index 1983-2023. Source: NOAA Fisheries and Pacific Fisheries Management Council. Note there was no harvest allowed in 2024, as in 2023.

American River Salmon Update – Delayed Spawning, November 2024

Posted on November 21, 2024 by Tom Cannon

In a 10/19/2023 post, I discussed how the lack of access to Folsom’s deep cold-water-pool results in delayed natural and hatchery spawning of American River fall-run salmon. During the 2020-2022 drought, Reclamation released water from the lower-level power bypass to provide the cold water (<55ºF) salmon need for spawning (see Figure 1). However, this fall 2024 Reclamation has chosen not to use the power bypass to release cold water (Figure 2), despite higher storage levels than during the recent drought (Figure 3). Lack of cold water delays natural spawning and hatchery egg taking, to the detriment of egg viability and fry production.

Figure 1. Water temperature of water released from Folsom Dam, Oct-Nov 2021. Late October drop in water temperature was from release of cold water from lower level outlet. Also shown is recent average for previous 7 years.

Figure 2. Water temperature of water released from Folsom Dam, Oct-Nov 2024.

Figure 3. Folsom Reservoir storage levels 2015-2024.

Figure 4. Photo of closed-gate entrance to Nimbus Hatchery fish ladder 11/14/2024.

Summer 2024 Operations of the Shasta/Trinity Division of the CVP

Posted on November 13, 2024 by Tom Cannon

Summer 2024 was an unusual summer in an unusual year for salmon in California’s Central Valley.

July 2024 was the hottest ever recorded on earth and in the Central Valley. Record high air temperatures occurred in early July throughout the Valley. A close look at July 2024 provides some valuable insights as to the future climate and salmon in the Valley.

July is an important month for Chinook salmon populations in the reaches of the rivers that are downstream of major dams. Winter-run salmon are at peak spawning in the Sacramento River near Redding (mainly the ten miles below Keswick Dam). Spring-run salmon are holding over the summer in the Trinity River below Lewiston Dam, in the Sacramento River below Keswick Dam, and in Clear Creek below Whiskeytown Dam. (Spring-run salmon are also holding in the Feather River below Oroville Dam and below falls on Butte, Deer, and Mill creeks.) Fall-run salmon have only just begun their journey from the ocean in the Sacramento and Klamath/Trinity rivers.

The goal in summer for the Shasta/Trinity Division of the federal Central Valley Project is to keep dam releases cold (around 50-52^oF) for winter-run spawning and egg incubation, and for holding adult spring-run salmon. Dam releases from the stored cold-water-pool supply are prescribed to accomplish the goal. The dams also release water for hydropower, for downstream water supply deliveries, and to meet requirements for salmon habitat and other environmental purposes.

Reclamation must balance these uses in July with protecting the salmon and other fish during the rest of the water year and with maintaining adequate storage for next water year. Reclamation released its draft environmental impact statement for the future long-term operations of the Central Valley Project operating earlier this summer – comments were due in September. Reclamation’s plan is not to meet the needs of the salmon except in wetter years – simply put, to “split the baby.” Reclamation’s proposal for how it will balance the needs of water users and the salmon will lead to the extinction of at least two runs of the salmon.

In the Central Valley, Water Year 2024 turned out to be above normal, after a wet 2023. Shasta and Trinity reservoirs nearly filled during the winter-spring – a good start to end-of-spring conditions. Shasta Lake started July with 4 million acre-feet (maf) in storage (out of a 4.5 maf capacity) and ended July with storage of 3.5 maf (Figures 1 and 2). Trinity Lake began and ended July with 2 maf in storage (out of a 2.5 maf capacity), after transferring about 100 thousand acre-feet (taf) to the Sacramento River in May-June and another 100 taf in July. Water temperatures of released water from both Keswick and Lewiston dams were maintained at the target 50-52^oF. The secret to this success was retention of sufficient storage and cold-water pool supplies in Shasta and Trinity reservoirs – a relatively easy task in an above normal water year after a wet year.

The challenge for Reclamation in the past, present, and future is to retain sufficient storage and cold-water-pool supplies to maintain the 50-52^oF dam release targets through the fall of all water year types, especially the drier years. Reclamation tried in the 2021-2022 drought, but grievously failed to meet the needs of salmon (Figures 2-4). Now Reclamation is asking the state and federal resources agencies for permission to explicitly plan to not meet the needs of the salmon in drier years.

Absent such an agreement to fail in drier years, Reclamation will have to reduce hydropower production/revenues and, most critically, the amount of irrigation deliveries to water contractors. It will have to reduce already dry-year-constrained water deliveries to retain more stored water and the necessary cold-water-pool supply for salmon. It will have to carry over more storage supply at the end of summer, have greater amounts stored by the end of spring, and deliver less water in many years from spring through fall. There is no choice if Reclamation is to meet promises and commitments to maintain the salmon populations in the Klamath/Trinity and Central Valley.

For a more insight on what the plan entails and how better to meet the needs of salmon, see CSPA’s alternative plan submitted in 2021 to save salmon in a drought year like 2021.

https://www.waterboards.ca.gov/drought/sacramento_river/docs/2021/cspa_tmp_052321.pdf

Figure 1. July 2024 conditions in the Shasta-Trinity Division of the CVP. Blue numbers are streamflows (cfs) and reservoir water storage levels. Green numbers are average water temperatures (degrees F).

Figure 2. May-October Shasta Reservoir storage levels in acre-feet 2021-2024.

Figure 3. Trinity River flows and water temperatures below Lewiston Dam 2020-2024.

Figure 4. Water temperature of Sacramento River below Keswick Dam 2021-2024. Note the cold-water-pool supply in Shasta Reservoir was depleted by the send of August in drought years 2021 and 2022 despite attempts to conserve the supply in spring by releasing warmer surface waters from the reservoir.

Butte Creek Spring Run Status – Fall 2024

Posted on November 4, 2024 by Tom Cannon

The spring-run Chinook salmon in Butte Creek had extremely low spawning runs in 2023 and 2024 (Figure 1).

In part, this was because all Sacramento River Valley salmon populations are collapsing due to the direct and indirect effects of the 2020-2022 drought and related management actions, on top of climate change and catastrophic fires.¹ Drought conditions in 2021 and 2022 in the spawning rivers, lower Sacramento River, Delta, Bay, and ocean all contributed to poor juvenile salmon survival.

The poor number of Butte Creek spawners in 2024 is also related to the high pre-spawn mortality of adult salmon in Butte Creek in 2021,² as a result of drought conditions during the winter-spring upstream migration and summer-fall holding and spawning.

Despite the failures of brood years 2020 and 2021, there is optimism for brood year 2022 and its spawning run in 2025 (Figure 2). Water year 2023 was a wet year, with good young survival conditions for juvenile salmon. Though brood year 2022 had only about 3700 spawners, , the returning adults were able to migrate and spawn with minimal stress in a drought year.

The uncertainty that remains is the survival of brood years 2023 and 2024, because of their potential small number of returning spawners in 2026 and 2027. Water year 2024 was a above-normal water year, but it was not without its stresses.³ Early indicators suggest 2025 could be a dry year. The potential for small runs to lead to strong brood years also leaves room for doubt given that four recent years of poor spawners led to poor recruitment (four dots at lower left in Figure 2).

The poor spawner numbers in 2023 and 2024, coupled with the uncertain forecasts for runs in 2025-2027, represent a serious population threat that calls for strong actions to save the species and rebuilding the spawning stock.

Winter Actions

Winter fry-fingerling emigration down lower Butte Creek past the Parrot-Phelan Diversion Dam and the primary screw trap counting station occurs in earnest beginning in mid-December, with a peak in January. The peak in fry emigration (the main element of juvenile salmon production from Butte Creek) occurs during early winter precipitation events. The fry, often still feeding on their yolk sac, leave the cold turbid creek heading for warmer, low-velocity food-rich floodplain waters of the Butte Basin and the Sutter Bypass, and for the tidewater of the Bay-Delta.

Strong winter growth is essential for good survival (good growth rates, and lower rates of starvation and predation). Strong winter growth promotes early smoltification and entry to the ocean. The main success factors in winter are adequate transport flow, access to and from floodplain habitats in the Butte Basin and Sutter Bypass, and low predation rates.

Spring Actions

Pre-smolt, sub-yearling smolts, and yearling smolts emigrate in modest numbers from Butte Creek in spring. These late migrants contribute to population numbers and genetic diversity. Success of these late migrants depends on high transport rates, low water temperatures, minimal diversion to often excessively warm floodplain habitats, minimal entrainment into unscreened water diversions, and minimum flow-through rates from river to floodplain habitats.

Adult spring-run salmon migrate from the Bay to upper Butte Creek in spring. They require adequate flows and water temperatures often not available in drought years, especially in late spring.

Specific Winter and Spring Actions to Consider:

Minimize water diversions at Parrot-Phelan Diversion Dam (and other creek diversions). In early winter, prioritize flow in Butte Creek over diversions for waterfowl pond flood-up and rice field decomposition (Figure 3), except in high runoff conditions. In spring, maintain flow in Butte Creek at the highest levels possible for attraction and holding except in early spring flood conditions.
Minimize the flow split into Sanborn Slough at bifurcation weir. Do not force more than 30% of Butte Creek flow into Sanborn Slough, which reduces important benefits of floodplain access and inundation.
Minimize diversions in Butte Basin and Sutter Bypass.
Keep Butte Slough Outfall closed except under Butte Creek flood relief conditions; instead, maximize flow through Butte Basin and Sutter Bypass.
In the event of dry-drought conditions, capture juvenile salmon at screw trap locations and Parrot Phelan Screen Bypass, and transport them to the mouth of Butte Creek, Verona, a conservation hatchery, downstream floodplain habitat, or a Bay-Delta location.
Maintain adequate transport flows in the lower Yolo Bypass and lower Sacramento River, and into and out of the Delta in winter, to maximize survival to the Bay and ocean.