Author Archives: Tom Cannon

WINTER-RUN CHINOOK SALMON A Plan for the Future

Posted on by

Photo 1. Keswick Dam – the upper extent of salmon in the Sacramento River. Source: USFWS

Winter-run Chinook salmon were once found throughout the Upper Sacramento River watershed, including the Sacramento, McCloud, and Pit River drainages, as well as in Battle Creek (Figure 1).  Following the construction of the Central Valley Project’s Shasta and Keswick dams in the 1940s, winter-run were confined to the lower Sacramento River below Keswick Dam.

Winter-run are one of four Chinook salmon subspecies found in the Central Valley.  As “winter-run,” the historical population took advantage of the Mediterranean climate’s wet winter and spring to migrate to and from the ocean to optimal spawning habitats in the Mount Shasta and Mount Lassen volcanic Cascade watersheds.

Adults returned from the ocean in winter and spring, reaching elevations near 3,000 feet on the west and south flanks of Mount Shasta in the upper Sacramento River, McCloud River, and Pit River.  Cold, clear spring waters sustained them until they spawned in late spring and summer.  Fry emerged from the gravel redds in early fall.  High winter-spring flows transported fry to the Lower Sacramento River, Valley floodplains and the Bay-Delta estuary that provided optimal winter rearing conditions (e.g., water temperatures from 10-15oC), with abundant food and cover in marshes, creeks, and sloughs.  The fry grew to ocean-ready smolt size by late winter and early spring and headed to the ocean.

The system was ideal, producing hundreds of thousands if not millions of adult winter-run salmon which many native peoples depended on for centuries.

But that all changed in the mid-20th Century when winter-run salmon populations were decimated by dams that blocked adult salmon access to their historical spawning grounds.  Winter-run salmon persisted in the Sacramento Valley below Shasta and Keswick dams in tailwater habitat sustained by cold-water releases from the depths of Shasta Lake, a modicum of spawning and rearing habitat, and – since 1998 – by one conservation hatchery. Much of the remaining spawning, rearing, and migration habitats were lost to mining, water diversions, roads, logging, and urbanization.

Winter-run salmon were nearly gone from the Sacramento River after the 1976-77 drought.  Cold-water habitat was not sustained below Shasta Dam in the drought, and escapement plummeted (Figure 2).  The escapement (returns) in 1979 and 1980 from brood years 1976 and 1977 was very low.  Brood year 1978, the offspring of brood year 1975 (which had been in the ocean during the drought) did well in wet year 1978 and returned well in 1981.  However, because of dry conditions in 1981, survival of brood year 1981 was poor.  The failures of brood years 1976, 1977, and 1981 (and their offspring) led to a general population collapse.

The subsequent 1987-92 drought led to the near extinction of the run and its listing as endangered under the federal and state endangered species acts.  Protections mandated in the listings, a decade of wetter years (1993-2003), some major improvement in CVP infrastructure and operation, and initial operation of the Livingston Stone Winter Run Conservation Hatchery in 1998 led to a partial recovery from 2001-2006.

The population declined again with the 2007-2009 and 2013-2015 droughts, with only partial recovery after two wetter periods (2010-2012 and 2016-2019).

The 2020-2022 drought caused poor brood year 2020 and 2021 fry production (Figure 3) and subsequent poor escapement in 2023 and 2024 (see Figure 2).  Emergency management actions in 2022, including the establishment of a new Battle Creek population and increased hatchery production, may have helped ameliorate some of the effects of the 2021-22 drought, leading to an increase in the 2025 returns (based on initial indications).  Despite its low fry numbers, brood year 2022 had good juvenile survival conditions in wet winter 2023 and good conditions for returning adults in above-normal water year 2025.  Also, closed fisheries from 2023-2025 contributed to strong 2025 escapement.  The good 2025 run and the good habitat conditions in 2025 resulted in strong fry production of brood year 2025 (Figure 3).

Many factors contributed to these long-term population trends, including negative factors such as overfishing, degradation and loss of freshwater and estuarine habitat, Shasta-Trinity hydropower operations, poor ocean conditions, disease, and hatchery practices.1 These include:

  • Overfishing – Though winter-run adults in the ocean are partially protected with closure of spring coastal fisheries near the entrance of San Francisco Bay, winter-run immature adults are not explicitly protected in other seasonal fisheries during their two-year period of ocean residence. Regional closures in ocean fisheries based on known ocean movements of winter-run are only partially effective.
  • Fall-winter rearing and out-migration habitat – Fall-winter habitat in the 200 miles of river and Delta habitat between Redding and the Bay are essential for winter-run brood year survival and smolt production to the ocean. Especially important are late fall and early winter movement to and through the Delta that are stimulated by stream flows and sustained by the first river flow pulse.2  Operation of the Delta’s Cross Channel gates and south Delta diversions restrictions play a very large role in successful outmigration (Figure 4).
  • Hydropower Operations – Shasta-Trinity Division hydropower operations affect real-time stream flows and water temperatures in the lower Sacramento River in the summer, fall, and winter seasons. Late-fall reductions in Keswick Dam releases at the end of the irrigation season limit both spawning and incubation habitat and flow-related downstream migration.
  • Poor Ocean Conditions – Poor Ocean conditions in 2007-2009 that contributed to the 2008-2009 crash of fall-run salmon also likely contributed to poor winter-run escapement.
  • Hatchery Practices – Hatchery practices for the most part have been beneficial to the winter-run population through the release of several hundred thousand sub-yearling smolts per year. However, releases near the hatchery in drier years help minimally because fewer hatchery smolts survive to the ocean.  Survival of coded-wire tagged winter-run hatchery smolts in dry years (Table 1) is only about 1/10th of that in wet 3  Survival is improved when hatchery smolt releases are coordinated with natural or prescribed pulse flows.4

Recommended Actions

Recovery recommendations are outlined in this section in three categories: habitat, hatcheries, and harvest.  The two main themes of the recommendations are (1) the best strategies for dealing with warmer, drier years and (2) improving population recovery after droughts.  These themes will require policy improvements for both drought and non-drought years.  The recommendations can be reasonably implemented based on the historical range and capabilities of winter-run salmon, but they may prove difficult under present political and social demands for water supply and project operations (e.g., hydropower peaking demands).

Lower Sacramento River – water temperature:  Maintain spring water temperatures in the Lower Sacramento River downstream from Red Bluff to the Delta (Freeport gage) at <65oF.  At all other times water temperature should be no higher than 68oF from Red Bluff to the Delta.

Upper Sacramento River – water temperature:  Maintain water temperatures at or below a maximum of 53oF in the Upper Sacramento River below Keswick Dam (river mile or RM 300) downstream to the mouth of Clear Creek (RM 290), and at or below a maximum of 56oF below the mouth of Clear Creek to the mouth of Battle Creek, and at or below 60oF from the mouth of Battle Creek to Red Bluff (RM 240).  (See Figure 5 for suggested standard/objective.)

Upper Sacramento River – streamflow:  Adaptively manage stream flow in the 6,000-10,000 cfs range depending on available cold-water pool supply and irrigation needs, fall-run salmon spawning, and the need to ensure that a late summer/fall stage drop does not lead to redd stranding for winter-run or fall-run salmon.  I recommend, at minimum, two pulse flows, each of 10,000 cfs minimum at Red Bluff, supported as needed by Keswick Dam releases, one in late fall or early winter coinciding with the first seasonal rains, and one around early February.

Sacramento River Base Winter Flow:  For the Sacramento River through the Delta, I recommend a base minimum flow of at least 5,000 cfs to maintain juvenile salmon transport and rearing habitat.

Delta:  The Delta Cross Channel (DCC) should be closed during fall flow pulses.  South Delta exports should be kept to a minimum during fall flow pulse.  Sacramento River Delta inflow (Freeport gage) should have a minimum daily (tidal) average flow of 20,000 cfs in late fall and winter.  Delta outflow should have a minimum daily (tidal) average flow of at least 10,000 cfs in late fall and winter.

Hatchery:  Release winter-run hatchery smolts to the Sacramento River and Battle Creek near Redding during flow pulses.

Hatchery:  Raise hatchery fry in controlled Lower Sacramento River floodplain habitats for volitional release during flow pulses.

Above Shasta Reservoir Trap-and-Haul:  More fully develop the trap-and-haul program to establish winter-run salmon subpopulations in (1) the spring-fed reach of the upper McCloud River above McCloud Falls, where stable water temperatures and stream flows are best for the logistical requirements of such a program; and (2) Ripley Creek, the South Fork Battle Creek tributary historically fed by Hazen Spring.  Offspring from such efforts can be readily trapped from these controlled flow spring creeks and returned to the hatchery for further rearing or release.

Fishery Harvest: Mark-selective fishery harvest rules could limit harvest of natural-born winter-run salmon.  Incidental catch (bycatch mortality) should be minimized in fishery areas frequented by adult immature and mature winter-run salmon through fishery restrictions.  Mark-selective harvest would involve large-scale investment in more complete hatchery marking throughout the Central Valley hatchery system, most of which currently marks only one quarter of hatchery production.

 

Figure 1. Winter-Run Chinook salmon Streams of the Central Valley. Source: NMFS.

Figure 2. Winter-run Chinook salmon escapement in the Sacramento River mainstem, 1970 to 2024. Note: Winter-run escapement is made up of the total of these components: (a) Winter in-river Battle Creek – upstream of CNFH: Fish passed upstream of Coleman Weir; (b) Winter in-river Clear Creek: not a stable breeding population; (c) Winter in-river mainstem Sacramento – downstream of Red Bluff Diversion Dam (RBDD): downstream mainstem numbers based on upstream estimates and redd distribution; (d) Winter in-river mainstem Sacramento – upstream of RBDD: upstream mainstem in-river estimates prior to 2001 were based on RBDD counts. Subsequent estimates are based on carcass surveys. Numbers using RBDD data are adjusted for angler harvest.

Figure 3. Winter-run juvenile production index (JPI) from Red Bluff trap collections 1992-2025. Data source: USFWS Red Bluff.

Figure 4. Hourly streamflow in the Delta Cross Channel and Georgiana Slough in the northern Delta, 2019-2022. Note that zero discharge at the Delta Cross Channel gage indicates the gates were closed.

Figure 5. Hourly water temperature in the upper Sacramento River above the mouth of Clear Creek (rm 290) in the May-July spawning season of winter-run salmon. Red line is the upper end of safe spawning water temperature for salmon.

Table 1. Tag returns for winter-run hatchery smolt release groups for brood year 2012-2014, with date released, release location, and estimated percent survival (escapement plus fishery catch). Note there were significantly higher survival rates for brood year 2012 (2013 release date) than brood years 2013 and 2014.

  1. (NMFS), West Coast Region (WCR). 2016. Viability Assessment for Pacific Salmon and Steelhead Listed under the Endangered Species Act: Southwest. Dated: February 2, 2016. Southwest Fisheries Science Center (SWFSC), Fisheries Ecology Division, 110 Shaffer Road, Santa Cruz, CA 95060. ↩
  2. https://calsport.org/fisheriesblog/?p=4034, https://calsport.org/fisheriesblog/?s=winter+run+salmon&submit=Search&paged=3 ↩
  3. https://calsport.org/fisheriesblog/?p=4096 ↩
  4. https://www.fisheries.noaa.gov/feature-story/sacramento-river-pulse-flow-expected-increase-survival-juvenile-salmon-traveling-ocean ↩

Sturgeon 2025 – A Retrospective

Posted on by

Tom Cannon December, 2025

In a 9/12/25 post, I warned of poor summer conditions in the Bay for sturgeon.  This came on the heels of a poor population status assessment by CDFW.

From the Department of Fish and Wildlife: “Recent results from white sturgeon monitoring surveys by the California Department of Fish and Wildlife (CDFW) suggest the white sturgeon (Acipenser transmontanus) population has continued to decline. CDFW fisheries biologists now estimate there are approximately 6,500 white sturgeon between 40-60 inches long in California — down sharply from the previous estimate of approximately 30,000 fish in that size range, based on the 2016-2021 survey average.” https://mavensnotebook.com/2025/07/10/cdfw-scientific-surveys-show-continued-decline-in-white-sturgeon-population/

Not only was the recent adult sturgeon population survey estimate down, but the products of sturgeon reproduction in 2025 were nearly non-existent, a pattern inconsistent with an above-normal water year.   During the wet year 2023, white sturgeon reproduction in the Bay-Delta population was up sharply, as shown by numbers salvaged at the south Delta pumping plant fish salvage facilities (Figure 1).  In contrast, sturgeon salvage numbers were very low in summer of above-normal water year 2024.  In above-normal water year 2025, no sturgeon were collected in the south Delta salvage surveys.

Figure 1. Number of juvenile sturgeon salvaged at south Delta state and federal pumping plant fish screens in wet year 2023. Source: https://wildlife.ca.gov/Conservation/Delta/Salvage-Monitoring

A 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 (Figure 2).  Water temperatures were above optimal (>65oF) and at times stressful (>68oF) or even lethal (>72oF) in 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 68oF 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.

The water temperature standard could be met if river flows are maintained in the 8000-10,000 cfs range at the Wilkins Slough gage (WLK) located upstream of the mouth of the Feather River (river mile 120). (Note the water temperature benefit of higher flows in the May and June flow pulses in 2025.)

Figure 2. Lower Sacramento River flow and water temperature at Wilkins Slough gage (RM 120) Apr-Jul 2023-2025. Stress on egg and larval sturgeon occurs above 65ºF, whereas mortality begins at 70-72ºF.

The residual adult sturgeon population within their Bay summer habitat also experienced unfavorable elevated temperature conditions (>20ºC, 68ºF; Figure 3).

Figure 3. Water temperature and salinity in Suisun Bay at the Benecia Bridge gage, Aug-Nov 2025. Water temperature spike in mid-September occurred with Delta draining in super moon cycle and low Delta outflow (without Fall X2 Action).

For further detailed discussion of the status of sturgeon in the Central Valley see:  https://calsport.org/fisheriesblog/?cat=20 .

Sacramento River Salmon Redd Dewatering – Fall 2025

Posted on by

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

Posted on by

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.

Reclamation plans to take more water from the Delta

Posted on by

A December 3, 2025 article in the LA Times warns of the federal government’s plan to take more water from the Delta. This is not something new – they have maximized exports much of this year and last year (Figure 1).  The State of California has also been doing this, but to a lesser extent (Figure 2).  Together, the two projects can export up to 22,000 acre-ft per day (8,000 acre-ft/day at Tracy, 14,000 acre-ft/day at Banks).  In a wet (2023) or above-normal year (2024 and 2025) exports can exceed 6-million acre-feet out of a potential maximum export pumping capacity of 8 million acre-feet.

The projects were able to exceed expectations in above-normal water year 2025 by eliminating the Fall-X2 Action that over the past decade required higher Delta outflows and lower exports in the September-October period to protect Delta smelt in the Bay-Delta.  In September 2025, the projects were able to export 674,000 acre-feet by dropping the Fall-X2 Action, compared to 536,000 acre-feet in September 2024 when the Fall-X2 Action was implemented.

The increased September exports in 2025 had significant environment effects that impacted salmon, smelt, and other Bay-Delta native fishes.

  • First, Delta outflow to the Bay was reduced in half (about 300,000 acre-feet, Figure 3) through a combination of the higher exports and lower reservoir releases (Delta inflow, Figure 4). That led to higher temperatures of water entering the Bay and the low salinity zone (LSZ) moving upstream from the Bay into the west Delta channel near Rio Vista (Figures 5 and 6).  These effects are detrimental to salmon at the peak of their fall migration into the Bay from the ocean and to the low salinity zone, which is designated critical habitat for smelt.
  • Second, lower Delta inflow from the Sacramento River (Figure 4) led to higher water temperatures in the north Delta at Rio Vista (Figure 6) and Freeport (Figure 7).
  • Third, reduced flows in the lower Sacramento River (Wilkins Slough, Figure 8) led to higher water temperatures (Figure 9), detrimental to salmon during their spawning migration to the upper Sacramento River and its tributaries.

In drier years (below-normal, dry, and critical), there are no Fall-X2 Actions, but there are many other restrictions on river flows, exports, and reservoir storage use to protect fish and their habitat as well as future water supplies.  In the past, Delta exports in drier years have been limited to only 3 to 5 million acre-feet per year.  We have yet to see the federal government’s plan to export more water in such years.  We can only guess as to what drastic changes to expect and the environmental damage that could ensue with the new federal export plan.  Higher spring exports in 2025 (see Figure 1) is one such change.

Figure 1. Federal exports from the south Delta via the Tracy Pumping Plant (TRP) in 2024 and 2025

Figure 2. State exports from the south Delta via the Harvey Banks Pumping Plant (HRO) in 2024 and 2025.

Figure 3. Delta Outflow to the Bay in Aug-Sept period of 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 4. Streamflow in the north Delta at the Freeport gage May-Dec 2024 and 2025. The Fall-X2 Action was implemented in September 2024 but not in September 2025 nor in October 2024 or 2025.

Figure 5. Salinity and water temperature in the west Delta near Rio Vista from August 2023 through September 2025 with emphasis on Sep-Oct period. Red lines denote water temperature (20C) above which there is significant stress on migrating adult fall-run salmon. The Fall-X2 Action was not implemented in October 2024 or September 2025.

Figure 6. Water temperature in the Sacramento River channel at the Rio Vista Bridge gage Aug-Sep 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 7. Water temperature in the Sacramento River channel at the Freeport gage in September 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 8. Streamflow in the lower Sacramento River at the Wilkins Slough gage in September of 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 9. Water temperature in the lower Sacramento River at the Wilkins Slough gage in September of 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.