Category Archives: Fish (general)

The Premeditated Murder of Sacramento River Salmon in Summer 2026

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The Bureau of Reclamation is systematically emptying Shasta Reservoir of its cold-water-pool reserve this summer. At the current and planned rate of release, Sacramento River winter-run, spring-run, and fall-run salmon broodyears 2026 will not survive the summer and fall.

The process employed by Reclamation is premeditated murder of salmon in response to the Presidential Executive Order 14181. That order requires federal agencies to “override existing activities that unduly burden efforts to maximize water deliveries.”

Reclamation’s 2026 Sacramento River Temperature Management Plan (TMP) already contained information that showed Reclamation’s predicted water temperatures for end-of-summer Shasta Reservoir releases to be wildly optimistic. Table 2 of the TMP showed a planned June-August release from Shasta Reservoir of 1.9 million acre-feet. 2 million acre-feet was the amount of cold water in Shasta Reservoir on June 1 (Figure 1 below: black line within second-darkest blue).

Reclamation knew that that the cold-water supply in Shasta was already compromised by poor snowmelt and runoff. Nonetheless, Reclamation released the draft TMP in May. Reclamation ignored concerns from state and federal resource agencies, and proceeded to finalize and implement the TMP.  Reclamation knew, or at the very least should have known, that it could not maintain 53.5ºF at the Clear Creek gage (CCR) and 56ºF at the Balls Ferry gage (BSF) even through August, let alone through September or October, with the planned level of releases from Shasta Reservoir for irrigation deliveries.

Can salmon be saved in 2026?

The CSPA 2021 TMP proposed a 5000 cfs release of 53-54ºF water from Keswick Reservoir, with no Trinity transfer through the Spring Creek Powerhouse, and with minimal daily peaking power production to limit withdrawals of warm water from the surface of Shasta Reservoir.  The approximate 10,000 acre-feet/day CSPA proposed in 2021 is roughly the amount of cool (<52F) water left in Shasta Reservoir on August 1, 2026. That release schedule would sustain relatively cool water in the Sacramento River through October (Figures 1 and 2).  This regime would maintain 54.5ºF at SAC and 56ºF at Clear Creek CCR at the control points through October. Though far from optimal, this would provide some minimal level of survival of broodyear-2026 salmon and provide an end-of-September Shasta storage level near 2.4 million acre-feet, as recommended by the State Water Board.

Figure 1. Shasta Reservoir’s daily isothermobaths (volume of storage) in 2026. Note Reclamation’s TMP EOS 2.2 MAF forecast. Source: sactemprpt-2.pdf.

Figure 2. Shasta Lake storage (acre-ft) in drought years 2015 and 2022, below normal 2020, and above normal 2026.

Flood Bypasses are Key to the Future of Wild Salmon in Sacramento River Valley Initial success of the Fremont Weir Big Notch

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The Big-Notch Project at the Fremont Weir came online in late 2025. In this post, I describe events in December 2025 that provided improved access for juvenile salmon to floodplain habitat in the Yolo Bypass through that new Big Notch.

The goal of notch projects at the Fremont and Tisdale weirs in the Sacramento Valley is to create greater access to floodplain habitats for juvenile winter-run Chinook salmon, as well as fall-run and spring-run, in the upper Sacramento River Valley. The Fremont Weir project, completed in 2025, now improves access for salmon into the Yolo Bypass. The Tisdale Weir notch project, when completed, will improve access of upper Valley salmon populations into the Butte Basin and the Sutter Bypass floodplains.

Background on Floodplains and Butte Creek

The recovery and success of Sacramento River winter-run Chinook salmon is tied to floodplain rearing and smolt production in the wettest years. There is great potential improvement for the survival of endangered winter-run salmon by providing improved rearing access to the Sutter and Yolo flood bypasses.

The remarkable recovery of Butte Creek’s wild spring-run Chinook salmon at the turn of the 21st Century provides an excellent example.

The turnaround in Butte Creek followed a decade of restoration activity in the creek and its floodplain by the US Fish & Wildlife Service, the California Waterfowl Association, the Nature Conservancy, CalTrout, Friends of Butte Creek, duck clubs, rice farmers, and many other collaborators.1 The secret to the success was opening the Butte Basin and Sutter Bypass so that juvenile salmon could rear in the floodplain habitat in early winter. This led to accelerated growth and high survival, which in turn allowed early entry of smolts into the ocean by late winter and early spring.

How the Fremont Weir Big-Notch Project Worked in its First Year

The first significant winter rains of 2025 brought a strong pulse of flow to the lower Sacramento River in late December (Figure 1). That pulse began entering the Big Notch at the Fremont Weir on December 21st (Figure 2). River flow (and flow exiting the Sutter Bypass) passed through the Big Notch through the end of December. River flow was only high enough to overflow the entire Fremont Weir on Dec 27 and 28 (Figure 3). Thus, most of the water flowing into the Bypass at the Fremont Weir passed through the Big Notch. Lesser but substantial amounts of warmer water also flowed into the north Yolo Bypass via the Knights Landing Ridge Cut (Figure 4).

Overflows into the Yolo Bypass (also including the Sacramento Weir) rapidly fill the Bypass (see maps). The Bypass floods to depths of 8-10 feet (Figure 5). The slowing of flows and spread of shallow water leads to rapid warming (of the colder river water) in the flooded Bypass (Figure 6). The warming extends to the lower Sacramento River channel in the north Delta at the Rio Vista Bridge (Figure 7), downstream of the Yolo Bypass’s outlet.

The warmer shallow Bypass habitats (optimal growth 52-56ºF) have high food production that supports increased growth and survival of juvenile winter-run emigrating to the ocean. Substantial numbers of juvenile winter-run salmon likely entered the Yolo Bypass during the December event through the new Big Notch (Figures 8 and 9).  The access to the floodplain habitat likely contributed to the higher winter-run smolt 2025 index of the winter-run Juvenile Production Estimate (JPE, Figure 10) and the annual Chipps Island Trawl Survey index (Figure 11). Winter overflows into the other flood bypasses and the relatively wet water year 2025 also contributed.

The Benefits of Notches in Flood Bypass Weirs

The principal benefits of weir notches are that they allow water to enter flood bypasses (overflows) at lower river stages (at stages up to 10 feet or lower), and thus earlier in the late fall or winter. These systems can also enable overflow events during dry winter seasons that would not typically experience overflows. They also allow overflows later in the winter season to enhance adult and juvenile migrations of all the salmon runs through the bypasses (Figures 12 and 13).

The notches can also sustain overflows between periods of normal weir overflows. This not only sustains the access, but also reduces potential for stranding of adult and juvenile salmon. It also maintains good habitat conditions, minimizing overheating or disconnection of bypass habitats.

The broader overall benefits of weir notches are improved smolt production to the ocean, greater sustainable ocean harvest, and improved spawner numbers (escapement).

Map of Sacramento River Valley with Flood Weirs and Bypasses.

Map of Yolo Bypass – (Note fishery monitoring program sites.)

Map of Colusa Basin Drain and Yolo Bypass Tule Canal flow pathway to Rio Vista Bridge.

Figure 1. Streamflow in the lower Sacramento River below Wilkins Slough in December 2025. Source: CDEC.

Figure 2, Streamflow in the Yolo Bypass downstream of the Big Notch in the Fremont Weir.in December 2025. Source: CDEC.

Figure 3. Overflow into the Yolo Bypass at the historical Fremont Weir in December 2025. Source: CDEC.


Figure 4. Streamflow in the Ridge Cut Slough (Colusa Basin Drain connection to the upper Yolo Bypass below the Fremont Weir in December 2025.

Figure 5. Stage in the Tule Canal of the Yolo Bypass at Lisbon gage in December 2025.

Figure 6. Water temperature at the Lisbon gage in the Yolo Bypass in December 2025.

Figure 7. Daily average air and water temperature and river stage at the Rio Vista Bridge of the Sacramento River channel of the north Delta in December 2025. Source: CDEC.

Figure 8. Daily catch of older salmon (non-fry, predominantly winter-run) in Tisdale Screw Trap and environmental conditions September 2025 to May 2026.

Figure 9. Daily catch of older salmon (non-fry, predominantly winter-run) in Sacramento River near Sacramento beach seines and environmental conditions September 2025 to May 2026.

Figure 10. Juvenile Production Estimate (JPE) of winter-run salmon entering the Delta by brood year.

Figure 11. Cumulative catch index of winter-run salmon in Chipp Island Trawl Survey In the east Bay by brood year.

Figure 12. Fry of spring-run and fall-run salmon would enter the Big Notch of the Fremont Weir under these conditions in January-February 2026. The Wilkins Slough flow of the Sacramento River of <30,000cfs indicates most of the flow that would enter the Bypass would be via the Big Notch. Note: Some flow at the Big Notch entrance would also come from the exit of the Sutter Bypass.

Figure 13. Flow (cfs) in the northern Yolo Bypass in winter 2026. Most of the flow came from the Big Notch. Bypass water temperatures (not shown) were best for salmon fry at 50-55ºF in the January period but reached stressful levels >65ºF in the March period.

Butte Creek Spring-Run Salmon – May 2026 Update

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Central Valley Spring-run Chinook Salmon. Central Valley spring-run Chinook salmon typically return from the ocean and enter the Sacramento River system from February through June. Spawning occurs in Sacramento River tributaries from mid-September through early October with genetically distinct populations known from Clear, Mill, Deer, and Butte Creeks. Central Valley spring-run Chinook salmon also spawn in the Feather and Yuba rivers. Juveniles emigrate soon after emergence as young-of-year, or remain in or near their natal streams and emigrate as yearlings. Yearlings typically emigrate with the first flow increases in the fall and early winter. Similar to winter-run, Central Valley spring-run Chinook salmon populations have suffered significant declines in size. They are state and federally listed as threatened. CDFW

Butte Creek is a moderately sized tributary of the Sacramento River, located in California’s Central Valley near Chico, CA (Figure 1). It supports a core population of the threatened spring-run Chinook salmon native to the Central Valley and Sacramento River. Over the past decade, the Butte Creek watershed has experienced some of the largest Sierra fires of recent record.1 Prior to this period, the spring-run salmon in Butte Creek had represented a successful recovery within one of the Central Valley’s few remaining undammed streams.

I last updated the status of the Butte Creek spring-run salmon in a November 2024 post.  The spawning runs in spring-summers of 2023 and 2024 had been devastatingly low after suffering in the most recent three-year drought (2020-2022).  Some recovery in the spawning population in 2025 and 2026 brings a measure of optimism.

Problems with Recruitment

Low runs in 2023 and 2024 (Figure 2) suggest that brood years 2023 (BY23) and 2024 (BY24) will make limited contributions to runs between 2025 and 2028. Fewer eggs and any poor survival rates (e.g., from the 2024 fires or Thiamine deficiencies) will restrict recruitment of age 2-4 spawners from both brood years, limiting their contributions (recruitment into) to the future runs.

Initial survey findings show that the runs in 2025 and 2026 had fewer contributions from BY23 and BY24. Instead, most of the fish came from BY21 and BY22 spawners, whose offspring thrived during the wet years of 2023 to 2025 and gained advantages from fishery closures in those same years. Preliminary information on the 2026 run (not shown in Figure 2) indicates a low run, with only modest numbers of age-4 BY22 spawners, and lacking the normally predominant age-2 (BY 24) and age-3 spawners (BY 23).

The Cause

The cause of depressed recruitment in 2023 and 2024 was most likely poor spawning and early survival conditions during drought water years 2020-2022 that affected brood years 2020-2024.  The poor 2023 run was likely the consequence of poor survival of their source spawning adults (prespawn mortality in 2019-2021), eggs laid (2019-2021), and juveniles reared (2020-2022) of BY19-BY21 affected by the drought conditions of fall 2019 through winter-spring 2022.  For example, conditions in 2020 were very poor from low flows and high water temperatures from spring to fall (Figure 3).  The failure of PG&E’s Butte Canal in 2023 may have also been a factor.

The cause of the poor 2024 run is more complicated, because the number spawners in 2021 was high.  Drought conditions in fall 2021 and spring 2022 likely contributed to poor reproductive success and low smolt production (Figure 4).  However, the 2023 and 2024 ocean fisheries were closed, which should have more than doubled the normal run size.  The 2024 massive Park Fire may have contributed to the poor run, with lower summer-fall flows and higher water temperatures (Figure 5) and high pre-spawn mortality.

Other factors related to escapement (run size) include ocean conditions (e.g., the warm water blob and Thiamine deficiency), fishery harvest (or lack thereof), conditions in the lower Sacramento River and Bay- Delta.  All factors acting together in combination is yet another factor, with each factor potentially contributing to the other factors.

Conditions in the lower Sacramento River and Bay-Delta are changing for the worse.  For example, 2026 has been a relatively wet year, but poor snowpack and low March precipitation has led to stressful river and Bay-Delta habitat conditions in March during the peak of the adult spring-run salmon migration from the ocean.  Delta inflow was too low and water temperatures too high from mid-March to early April in 2026, almost as poor as drought year 2022 (Figures 6 and 7).  This problem led the Bureau of Reclamation to release a pulse flow from Shasta Dam in early April 2026 to help migrating salmon in the Sacramento River and its tributaries.

Solutions

The improvement of reliably robust runs of spring-run Chinook salmon is bound up in ongoing debates on how to manage Butte Creek salmon and their habitat.  Resource enhancement funds are scarce.  There is significant mitigation funding available from the PG&E 2023 flume failure that could play an important role.  More on solutions in upcoming posts.

Figure 1. Current distribution of spring-run Chinook salmon as reported by CDFG, 1998.

Figure 2. Butte Creek spring-run salmon escapement estimates by surviey 2001-2025. Source: CDFW.

Figure 3. Butte Creek water temperature and streamflow at USGS BCK-gage near Chico Feb-Oct 2020. Water temperatures above 18-20C are stressful to migrating and holding adult salmon.

Figure 4. Butte Creek water temperature and streamflow at USGS BCK-gage near Chico Aug 2021 to Jun 2022. Water temperatures above 18-20C are stressful to migrating juvenile salmon and holding adult salmon.

Figure 6. Flow in the Sacramento River at Freeport at the entrance to the north Delta in spring 2022-2026. Red line is recommended minimum Freeport flow. Source: CDEC.

Figure 7. Water temperature(F) in the Sacramento River at Freeport in the north Delta in spring 2022-2026. Red line is recommended maximum Freeport water temperature for spring salmon migrations. Source: CDEC.

Once again, Sturgeon overlooked in Spring 2026

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Water temperatures are reaching lethal levels (22oC) for the newly spawned sturgeon eggs and fry in the lower Sacramento River. To save this broodyear of sturgeon, resource managers must immediately increase flows in the lower Sacramento River. Right now, those flows are unusually low.

The San Francisco Bay-Delta watershed is home to two native sturgeon species: white sturgeon and green sturgeon. White sturgeon are popular among sport fishers in major rivers and the Bay-Delta. Green sturgeon are less common and are protected under state and federal endangered species laws, making their harvest illegal.

Both species migrate from the ocean or Bay into rivers to spawn—a behavior known as anadromy. Green sturgeon tend to spend more time in marine environments and travel further upstream to reproduce. White sturgeon are larger and sought after by anglers. Both types feed along river and bay bottoms, often attracted by bait that has a strong scent. The introduction of non-native clams has given sturgeon an abundant food source, potentially boosting their growth. However, they are sensitive to warm water and thrive best in cooler, saltier environments below 68°F (20°C).

Spawning poses significant challenges for sturgeon. They use stored energy in late winter and spring to reach clean, cool, fast-flowing rivers with deep, rocky bottoms where they lay sticky eggs. After several days, these eggs hatch. The young fry drift down to the Delta and Bay over about a month, feeding and growing along the way. Their survival depends on river conditions—low flow and warm water can be fatal in dry years. During wetter years, strong currents help them safely reach the Bay.

Once in the Bay, sturgeon can take 10 to 15 years to mature before returning upstream to spawn. Unlike salmon, sturgeon live long lives and can reproduce multiple times.

The frequency of wet years and the quality of Bay conditions both affect how many adult sturgeon persist in the population. Recently, recreational fishing has removed about 5–10% of adults annually. Droughts pose bigger risks—especially to white sturgeon—by warming Bay waters and encouraging algae blooms that deplete oxygen, sometimes causing mass die-offs during the summer.

Measures needed to support sustainable sturgeon populations amidst climate change include maintaining adequate river flows and suitable water temperatures in the Sacramento River, Delta, and Bay. This is especially important during spring and early-summer spawning and rearing periods.

Under current water management, most young sturgeon fail to survive the Delta due to poor flows, high temperatures, predation, and entrainment into water diversions. Summer is a critical season in the Bay, where most sturgeon reside, and healthy conditions are vital. Some years, large tides associated with Super Moons bring warm water into the Bay, triggering harmful algal blooms. Consistent freshwater inflow is necessary to support the food web and keep the Bay cool and oxygenated.

During consecutive dry years, population maintenance involves options like hatchery releases, rescuing stranded sturgeon, and stricter controls on fishing. The top priorities should be protecting breeding adults over 15 years old, ensuring adequate recruitment of younger subadults, and improving the survival of eggs and juveniles. Achieving these goals requires enhanced scientific monitoring and assessment of both the fish and their habitats, as is commonly recommended for other native fish like salmon and steelhead.

The current status of sturgeon is less well documented than other species like salmon, steelhead, smelt, and striped bass. Unlike others, there is no formal recovery plan for sturgeon. There are increasing calls to end the sport fishery and list white sturgeon as endangered. However, some scientists and resource managers argue that more pressing threats should be addressed first, and recommend focusing on gathering data from the fishery and data on population abundance.

In my last post on the sturgeon (February 2026), I hypothesized that the big reason for the unsuccessful sturgeon reproduction in water years 2024 and 2025 was poor conditions in the spring spawning and early rearing reach of the middle Sacramento River.  Water temperatures were above optimal (>65oF) and at times stressful (>68 oF) or even lethal (>72 oF) in spring 2024 and 2025.  Few juvenile sturgeon survive to reach the Delta under these habitat conditions.  This was one of the factors that led the State Water Board and USEPA to set 68 oF as the water quality standard for the Sacramento River two decades ago. This standard is also a condition of the State Water Board water right permits for the state and federal water projects.

Once again, during a relatively wet winter-spring, both the sturgeon and the water quality standard seem to be overlooked (see Figure 1).

To save this broodyear of sturgeon, resource managers must immediately increase flows in the lower Sacramento River. Right now, those flows are unusually low.

For more on white sturgeon science, monitoring, and fisheries management see https://wildlife.ca.gov/Conservation/Fishes/Sturgeon/White-Sturgeon.

Figure 1. Sacramento River streamflow and water temperature at Wilkins Slough in the lower prime spawning reach of white sturgeon in spring 2026.

Figure 1. Sacramento River streamflow and water temperature at Wilkins Slough in the lower prime spawning reach of white sturgeon in spring 2026.

Yuba River Fall-Run Salmon Crash 2016-2025

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The Yuba River Fall-Run Chinook salmon population “crashed” in the last decade.  Yuba River escapement ranged only from 2000-5000 spawners counted per year (Figure 1).  Such low escapements were last encountered only during the Central-Valley-wide crash during the 2007-2009 drought.

The decade-long low escapement reflects the effects of two droughts (2013-15 and 2020-22). Though the 2023-to-2025 escapements have increased slightly1 despite the 2020-2022 drought, the higher escapement reflects the benefit of fishery closures from 2023-2025 (fisheries normally harvest more than 50% of the adult stock).  Yuba escapement also reflects substantial numbers of hatchery strays from other rivers, including the Mokelumne and American River hatcheries, the Coleman hatchery on Battle Creek in some years, as well as the Feather River (Oroville) hatchery.  Small numbers of spring-run Feather hatchery strays from release locations near the mouth of the Yuba on the Feather River are also included.

The highest number of strays in the 2020-2022 period were from one group of Mokelumne River hatchery smolts released in 2018 to Half Moon Bay on the coast south of San Francisco.  The next highest group of strays are from American and Feather hatchery smolt releases to San Francisco Bay.  The trucked hatchery smolts do very well during drought years and thus tend to bias high the Yuba returns from drought years.  That is to say, drought effects on the natural Yuba run are even worse than indicated in escapement estimates.

I categorize the decade-long decline as a “crash” based on the population spawner-recruit (S/R) relationship (Figure 2).  The S/R “curve” generally reflects a positive logarithmic relationship between spawner and recruitment numbers.  The more eggs spawned generally leads to more adult returns three years later.  The S/R ratio, at least in the Central Valley salmon populations, also reflects drought or habitat conditions wherein recruits are generally depressed from density-independent habitat factors like droughts.  The six drought years in the last decade shown in Figure 2 as red dots have led to escapement levels in the lower-left quadrant of the S/R curve – a pattern often referred to as a population crash.

Often it is difficult for a population to recover from that situation because there are not enough spawners (eggs) to get the population out of the hole.  It would take a lot of good years in sequence to make that happen, unless certain actions are taken to accelerate the recovery.  For some suggestions on how this can be accomplished, see my past post on the subject.

Because of the supplementation of recruitment from other rivers and resulting mixed bag of spawners, the Yuba run is not threatened with extinction.  However, in its present state, its poor contribution to the commercial and recreational fisheries is a problem.  The Yuba is a magnificent salmon river that should contribute more salmon.

Figure 1. Yuba River Fall-Run Chinook salmon escapement estimates 1953-2024.

Figure 2. Yuba River Fall-Run Chinook salmon spawner-recruitment relationship wherein recruits are related to recruits three years earlier. Red dots represent escapement years where two years earlier it was a drought year during rearing and outmigration.