Category Archives: Chinook Salmon

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.

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.

Sacramento River Salmon Redd Dewatering – Fall 2025

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I have previously reported on the dewatering of fall-run salmon redds in the upper Sacramento River near Redding during the early fall spawning season. Redd dewatering has a significant negative effect on salmon egg and fry production that translates to lower annual escapement and significantly contributes to the multi-decade decline in the population (Figure 1).

Figure 1. Escapement to the upper Sacramento River natural spawning area 1952-2024.

October is the peak in the fall-run Chinook salmon spawning season (Figure 2).  During early November 2024, the Bureau of Reclamation reduced Keswick Dam releases from the October average of 7000 cfs to 4000 cfs.  The flow reduction reduced water levels in the upper river spawning grounds below Keswick Dam from approximately the 11-ft water surface elevation (stage) to about the 8.5 ft level, a drop of about 2.5 feet.  In 2025, nearly identical flow management led to the same redd dewatering conditions (Figure 3). With most of salmon redds constructed in the 1-to-3 ft depth range, most were dewatered or only slightly watered and thus susceptible to high-egg-mortality conditions (low flow, warm water, low oxygen, and sedimentation).

The flow management strategy was also employed in recent wet years 2017 and 2019, although a more benign strategy was employed in historical wet year 2011 (Figure 4).  The issue has attracted inter-agency study and mention, but actions necessary to reduce the problem have been limited.

Figure 2. Stage and water temperature in the Sacramento River below Keswick Dam in fall 2024. Grey box denotes period when most fall run salmon spawn in the upper Sacramento River.

Figure 3. Stage and water temperature in the Sacramento River below Keswick Dam in fall 2025. Grey box denotes period when most fall run salmon spawn in the upper Sacramento River.

Figure 4. Stage and water temperature in the Sacramento River below Keswick Dam in fall of wet years 2011, 2017, and 2019.

American River Salmon Update – Spawning Season, November 2025

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In a 10/19/2023 post and a 11/21/2024 post, I discussed how the lack of access to Folsom Reservoir’s deep cold-water pool results in delayed natural and hatchery spawning of American River fall-run salmon.  Delays, and spawning in warmer water, cause reductions in spawning success, smolt production, recruitment into harvestable fishery stocks, and spawning escapement (run size) to the American River.  Lower salmon contributions from the American River significantly reduce California coastal and river salmon fishery stocks.  Poor production in the American River contributed to the closure of California salmon fisheries in 2023-2025.

During the 2020-2022 drought, Reclamation released water from the lower-level power bypass (sacrificing hydropower production) to provide the cold water (<55ºF) salmon needed for spawning in the ten-mile spawning reach from Nimbus Dam (near Fair Oaks gage) to the William Pond gage (Figure 1).  This is the prime spawning reach for salmon in the lower American River.  However, in the fall of the wetter years 2023-2025, Reclamation did not use the power bypass to release cold water (Figures 2 and 3), despite higher storage levels than during the drought (Figure 4).  The lack of cold water delayed natural spawning and hatchery egg taking, to the detriment of egg viability, fry production, and smolts reaching the ocean.

Ultimately, the number of adult salmon returning to the American River to spawn (escapement) is the important measure of success.  There are many factors that may contribute to the number of returns.  Recent returns are up (Figure 5).  The 2023 and 2024 returns were good despite having been the product of the 2020-2022 drought reproduction (Figurer 6).  Closed fisheries in 2023 and 2024 contributed to higher escapements.

I also believe efforts to improve fall water temperatures below Folsom during the drought improved both the wild and hatchery components of escapement.  I remain concerned that a return to warmer fall water temperatures will hinder future escapement.

I am also concerned with apparent efforts to sustain higher fall 2025 reservoir levels (see Figure 4) by reducing tailwater stream flow rates (Figure 7).  Such low flows reduce the quantity and quality of salmon spawning habitat.  Many critical spawning side channels become dewatered at such low flows1.  Main channel velocities, substrate, and depths are also compromised at low flow rates.

Reclamation  also reduced funding for the salmon hatchery and for river habitat projects in 2025, and will likely do the same in subsequent years.  This strategy will not help to recover American River salmon stocks to levels that once again can contribute toward commercial and recreational salmon fisheries.

Figure 1. Map of three CDEC gaging stations on the lower American River.

Figure 2. Average daily water temperatures in Nov-Dec period at William Pond gage 2021-2025. Red line (55ºF) denotes upper safe level for Chinook spawning.

Figure 3. Average daily water temperatures in November period at Fair Oaks gage 2021-2025. Red line (55ºF) denotes upper safe level for Chinook spawning.

Figure 4. Late summer and fall Folsom Reservoir water storage (acre-feet) 2021-2025.

Figure 5. Adult salmon escapement estimates for the American River 1975-2024. Source: Grand Tab.

Figure 6. American River spawner/recruit relationship – { log10(escapement) -3.5]. Number is year of escapement (recruits). Color denotes water year type two years prior. Red is dry, green is normal, and blue is wet. Note escapement in 2023 and 2024 are red, denoting spawning and rearing occurred two years earlier in dry water years.

Figure 7. Streamflow (daily average) in the American River at Fair Oaks gage Aug-Nov period 2021-2025.