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.

Yuba River Fall Run Salmon – Status Winter 2023

Posted on March 19, 2023 by Tom Cannon

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.

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.

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:

those broodyear 2011 adult females;
their broodyear 2014 eggs and their hatchlings in summer-fall 2014;
the surviving broodyear 2014 fry in winter 2015; and smolts in spring 2015;
the yearlings, two-year-olds and three-year-olds in the ocean; and finally
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.

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.

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

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

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

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.

https://yubariver.org/posts/slow-start-to-the-salmon-season-in-the-lower-yuba-river/ ↩

Sacramento River Salmon Harvest Forecast: More Bad News

Posted on March 1, 2023 by Tom Cannon

The harvest of Sacramento River fall-run salmon – the largest of California’s dwindling salmon runs – is managed by both state and federal agencies and is based on past-to-present figures of long-term adult escapement (i.e., fish that aren’t caught and survive to spawn) (Figure 1).

The harvest is coordinated under the Pacific Fishery Management Council (PFMC), because many of the ocean fisheries take mixed stocks from both the US states and Canadian provinces. The “fishable” Sacramento River fall-run population is defined as the total number of adults in the ocean and rivers available for harvest in the ocean and rivers. The harvestable stock is defined as adults. It does not include grilse (salmon returning to freshwater after a single season at sea), whose harvest is generally not allowed.

Chart showing past-to-present figures of long-term adult escapement

Figure 1

The PFMC has declared an adult salmon escapement of 122,000-180,000 as a target goal range, a figure that theoretically provides a sustained yield for the fishery. However, because escapement estimates are not made until the end of the fishery harvest, total escapement has usually fallen below the maintenance goal – especially during drought years or after multiyear droughts.

In some years, sanctioned harvests have led to over-fishing (e.g., 2007, Figure 2). This is because the harvest control rules the PFMC employ are often based on inaccurate estimates of the size of the harvestable stocks and the relative effectiveness of the fisheries – how good the fisheries are at catching salmon (very good, it turns out).

Together, these harvest model errors and biases have led to over-fishing. This is not a new problem. Excessive harvests contributed to closure of the ocean salmon fishery off California in 2008 and 2009.

The PFMC and its constituent states and provinces are now developing harvest control rules for the 2023 fisheries. For the Sacramento River fall-run population, the preliminary estimate of the 2023 harvestable stock is approximately 180,000 fish; accordingly, the PFMC is anticipating a sanctioned harvest, and is now preparing harvest control rules.

But it would be a grave mistake to authorize a 2023 Sacramento River fall-run harvest; there should be no harvest allowed this year. Why? There are multiple reasons.

First, the 2019 to 2022 population trend was decidedly downward (Figure 1), and the salmon stock was overharvested in 2021 and 2022. Also, water year 2021 was a critical drought year that led to poor survival of the 2020 brood year fish. Due to drought conditions, 2021 brood year salmon experienced poor spawning, incubating, rearing, and emigration conditions. As a result, the fishable brood year 2020 and 2021 stocks now in the ocean are likely small, and their return to their natal rivers will likely be minimal. Indeed, the return (escapement) numbers for the 2020 brood year fish could be even lower than those for 2009, 2017, or 2022 – all abysmal years for returning salmon.

The bottom line: prospects for recovering a wild or natural-born salmon population in the Sacramento River and its tributaries will be substantially diminished if a salmon fishery is allowed in California this year.

Chart of the Sacramento Index and relative levels of its components.

Figure 2. Note harvest in 2007 and 2015-2017 resulted in failure to meet escapement goal of 122,000 adult salmon.

Table of the performance of Chinook salmon stocks in relation to 2022 preseason conservation objectives.

Figure 3. There was a fishery in 2022. Note 60,000 escapement for 2022 was only a third of the target goal of 180,000.

Smelt Status – Winter 2023 How Low Can You Go?

Posted on February 19, 2023 by Tom Cannon

In prior posts in December 2022 and November 2021, I described the status of listed delta smelt and of longfin smelt. More recent information shows little change in the dire outlook for these two native Bay-Delta fish (Figures 1-4).

Delta smelt and longfin smelt populations have declined severely over the past few decades due to poor water management. In the Bay-Delta, where the smelt spend most of their lives, south Delta water exports and warming of the Bay and Delta from reduced inflow and outflow has limited their production. Temporary urgency change petitions (TUCPs) during multiyear droughts and subsequent orders by the State Water Board have allowed reduced Delta outflow, leading to higher water temperatures and increased Delta salinity. The State Board is again considering yet another TUCP in winter 2023 that would reduce Delta outflow to allow higher exports.

In this winter 2023, the Low Salinity Zone has again moved further upstream (eastward) into the Delta because of falling freshwater inflow to the Delta after the January storms. Delta exports have fallen with lower Delta inflows as State Board conditions kick in. The TUCPs are an obvious and direct threat to these population remnants living in the Low Salinity Zone. Further allowing these weakened standards to be violated is a direct disregard for these nearly extinct species. Water management places them at extraordinary risk by (1) bringing them further into the Central-Delta zone of the two large South-Delta water diversions, (2) degrading smelt habitat with lethal water temperature, (3) further degrading their already depleted food supply, and (4) increasing the concentrations of toxic chemicals being relentlessly discharged into the Delta.

The scientific literature, and water and resource management agencies, all recognize these major problems. Many management and recovery schemes have been developed and implemented over the decades. However, nothing has stopped water managers’ relentless excessive use and abuse of the Central Valley hydrology. The salmon, smelt, sturgeon, and steelhead are not just the victims but serve as “canaries in a coal mine”, all dying while the water is continually mined from the system. Meanwhile, water managers blamed this mass extinction event on on climate change, cynically gaming worsening conditions to extract even more water.

There is more and more talk of employing “ecosystem-based management” that integrates the environment into all phases of decision-making, effectively giving the environment a seat at the table. But the reality is more like giving the chickens a say in how the foxes manage the depopulation of the hen-house. There is also talk about providing more flexibility in how and when water is used – allocating environmental water as “functional flows” or “environmental water storage” to optimize the ecosystem benefits of what little water is allocated for the environment. Placed in he hands of water managers, such efforts simply give them more flexibility to game the system to their advantage. When they think they can get more water, they just ask for it and usually get it. One policy group proposes: “Making this work may require establishing assets for the environment—such as water budgets, reservoir storage space, and funding to restore physical habitat—that can be flexibly used to adapt to changing conditions.” No, a piece of bread and a cup of water on the survivors’ deathbeds are all they get. Even the water managers get to choose the physical habitat and how its restored, and how much extra water they can take as a result.

It is time to change this pattern of abuse of public trust resources by standing up to abusers in the State’s TUCPs, the Update of the Bay-Delta Water Quality Control Plan, and the public review of the Delta Tunnel Project. The Tunnel simply adds another straw in the Delta, but further upstream, closer to the mouths of the Feather and American rivers, the main sources of Bay-Delta freshwater inflow.

Figure 1. Bay-Delta fall-midwater-trawl longfin smelt catch index 1967-2022.

Figure 2. Longfin Smelt Fall Midwater Trawl Index in recent two decades 2001-2022.

Figure 3. Log-Log relationship for longfin smelt index year (number shown are brood year “recruits”) vs index two years prior (spawners). Red numbers represent brood years that were the product of dry water years, green numbers = normal water years, and blue = wet water years. Blue dots are six most recent years, 2017-2022: fewer spawners produce fewer recruits.

Figure 4. Catch of Delta smelt in 20-mm Survey in late March 2022. Seven were captured in the north Delta just upstream of where adult hatchery smelt were released in December 2021.

Missing an Opportunity Downstream of Shasta Lake Late Fall – Early Winter Pulse Flow for Salmon Needed

Posted on January 2, 2023 by Tom Cannon

Juvenile winter-run, spring-run, fall-run, and late-fall-run salmon need a flow boost in the fall and winter to help them emigrate 300 miles down the Sacramento River from their spawning area below Shasta Lake to and through the Bay-Delta.¹ Yet while winter storms have now caused massive runoff downstream, the spawning reach of Sacramento River remains at its minimum flow. Even small pulse releases from Shasta and Keswick reservoirs during storms would start hundreds of thousands of juvenile salmon on their way to the ocean.

Historically, more than 50% of salmon spawning in the lower Sacramento River took place downstream of Clear Creek (Figure 1). That distribution has now changed, with over 90% of the spawning upstream of the mouth of Clear Creek in the 20 miles of river downstream of Keswick Dam. This change is a consequence of water management that confines suitable spawning habitat in summer and fall to the uppermost river reach.

Many juvenile salmon begin their migration to the ocean when the first fall rains create a pulse in streamflow. These fish include winter-run and late-fall-run smolts, and fall-run and spring-run fry. The first fall rain-induced flow pulse has been long recognized as an important functional flow event for all four salmon runs. For many decades, the fall pulse was recognized as an important feature needed in salmon management to ensure good survival of smolts to the ocean.

The fall pulse has often been forestalled in recent decades both by droughts and by water management. When the fall pulse comes, it comes only from upper river tributaries. But the natural salmon production cycle in the upper 20 miles of the spawning reach misses out on the flow benefit of fall rains. All runoff is captured in Shasta Reservoir. While downstream reaches receive tributary rainfall-induced streamflow (Figure 2), the upper river receives no pulse from Shasta Reservoir despite significant inflows (Figure 3). This factor alone is a key factor limiting natural production of the four salmon runs in the upper Sacramento River.

Lack of flow from Shasta also limits the effectiveness of the overall flow pulse (Figures 4 and 5) that carries the juvenile salmon downstream to the estuary. The upper Sacramento River, McCloud River, and Pit River flow into Shasta Lake. These major spring-fed rivers are the largest contributors of natural flows to the Sacramento River watershed, especially in drier years. They have not provided any the mainstem streamflow to the Bay-Delta estuary as yet this year. This pattern is generally true in all but the wettest water years.

Shasta Lake gained about 40,000 acre-feet in the first fall storm (Figure 6). A pulse flow of 5000 cfs for three days (an increase of approximately 2000 cfs for 72 hours) would have amounted to approximately 12,000 acre-feet, or roughly 30% of the water gained and (0.8% of the total storage). Considering that much of the first storm fell as snow, water managers could have reasonably have executed such a short pulse..

The second storm has delivered Shasta Reservoir another 100,000+ acre-feet. With a wet forecast for January, it is now time to release a least a short pulse from Shasta to move juvenile salmon downstream to where they can surf the tributary inflow to the Sacramento River downstream to the Delta. It is not too late. Before the storm that began December 29, most of the juvenile salmon remained upstream of Red Bluff or downstream in the river above the Delta,² as few had shown in Sacramento seines and trawls (data not shown).

Figure 1. Upper Sacramento River and historic salmon spawning distribution by percent by region. River-mile shown in parentheses. (Data source: CDFW)

Figure 2. Fall river flows at seven locations from Keswick Dam RM-300 (KWK), Bend RM-250 (BND), Hamilton City RM 200 (HMC), Colusa RM-144 (COL), Wilkins Slough RM-140 (WLK), Verona RM-80 (VON), and Freeport RM-50 (FPT) in the Delta.

Figure 3. Shasta Reservoir inflow and outflow in December 2022. (Data source: CDEC)

Figure 4. Screw-trap catch of fry spring-run and fall-run salmon with environmental data in fall 2022 at three locations in lower Sacramento River.

Figure 5. Screw-trap catch of winter-run fry-smolt salmon with environmental data in fall 2022 at three locations in lower Sacramento River.

Figure 6. Shasta Reservoir storage level in Nov-Dec 2022.

Central Valley Hatchery Salmon Production Is Being Wasted A Tale of Two Hatchery Salmon Smolt Release Groups

Posted on December 11, 2022 by Tom Cannon

There are two common strategies for releasing juvenile salmon from state and federal salmon hatcheries in the Central Valley. One strategy is the release of hatchery salmon smolts at or near the hatchery where they are produced. The other strategy is trucking the smolts from the hatchery and releasing them into the Bay. There is much controversy and argument over the relative merits of the strategies. There can be little argument that release into the Bay generates far more adult salmon than release near the hatcheries.

Consider what occurred with two American River release groups after their release in May 2018 and return as adults in 2020. Release group #061465 was 669,000 fall-run smolts (3-4 inches long) that were transported 20 miles downstream from the American River (Nimbus) Hatchery and released into the mouth of the American River under the Jibboom Street Bridge. Release group #061467 was 650,000 fall-run smolts transported approximately 100 miles downstream to net pens at the Wickland Oil Terminal for release into eastern San Pablo Bay, about 20 miles from the Golden Gate Bridge and the Pacific Ocean.

The estimated percent survival based on tag recoveries was 0.04% for group #061465 (released near the hatchery). The estimated percent survival was 2.20% for group #061467 (released in San Pablo Bay). The returns by locations are shown in Figures 1 and 2. These relative results are common.

Figure 1. Returns for tag group #061465.

Figure 2. Returns from tag group #061467.