Water Year 2023 (10/1/22-9/30/23) in the Central Valley was very wet, with exceptional hydrology. With the state’s salmon fishery closed and plentiful water there had been some optimism for the 2023 salmon runs. But there was also concern as to how much this year’s salmon runs would be affected by the poor water years 2020-2022.

The Mokelumne River system is achieving hoped-for outcomes from its salmon management. Over 20,000 salmon adult salmon have been counted moving upstream past the Woodbridge counting facility. The counting facility on Battle Creek has counted only about 5,000 salmon, in a system whose adult return are generally far greater than those on the Mokelumne. What happened?

1. Reasons for Strong Run in Mokelumne River – News reports and interviews with hatchery managers indicate a record high escapement of fall-run salmon to the Mokelumne River and hatchery. Factors that likely contributed to the strong run include the following:
   1. Of the 21 million fall-run smolts produced and released by the Mokelumne Hatchery during drought years 2020-2022, about half were released to coastal harbors and half released to Sherman Island sites on the lower San Joaquin River channel in the Delta (Table 1). These releases likely made up the vast majority of Mokelumne River returns in 2023 of age 2-4 adult returns.¹ Past survival rates for such coastal and Delta releases are among the highest for Central Valley hatchery fall-run salmon smolt releases. Coastal releases regularly have survival rates 5 times the rates of the Delta releases and 10 or more times the rates of Mokelumne River in-river releases. No releases were made to the Mokelumne River below the hatchery from 2020-2022. Straying rates of adults returning from the Mokelumne Hatchery off-site smolt releases often exceed 50%, with most going to the American River and lesser amount returning to the Feather and Merced rivers. Strays from hatcheries on those rivers also return to the Mokelumne River.
      b. The Mokelumne River has prescribed summer-fall attraction flows for fall-run salmon (Figure 1). However small in magnitude, they seem to attract adult salmon.

2. Reasons for Poor Winter-Run and Fall-Run Salmon Runs in Upper Mainstem Sacramento River and Battle Creek – News reports and hatchery news releases indicate a very low run for salmon in Battle Creek and the upper Sacramento River in 2023.
   1. a. All hatchery smolt releases from the Coleman Fish Hatchery on Battle Creek and the Livingston Stone Fish Hatchery on the Sacramento River in Redding in 2020-2022 were to the upper river near the two hatcheries. In prior years, survival was low for river releases in drought years and higher for Bay-Delta releases (Table 2).
   2. River conditions in the Sacramento River are generally poor (high water temperatures and low flows) in drought years like 2021 for late winter and early spring hatchery releases and wild salmon emigration. Overall outmigration success in every year but one has been poor since 2008, and is trending downward (Figure 2). However, in late winter and early spring 2021, a natural flow pulse occurred in the upper river that helped move the hatchery and wild smolts downstream (Figures 3 and 4).
   3. Water temperatures in the lower reaches of the Sacramento River were high when adult salmon were migrating upstream towards the upper Sacramento River and Battle Creek (and hatchery) (Figure 5).

Table 1. Tag groups of Mokelumne Hatchery fall-run smolts released in spring by location in 2020-2022 (brood years 2019-2021).

Figure 1. Streamflow of lower Mokelumne River at Woodbridge gage in water years 2020-2022 and long term average. Note October attraction flows and winter pulse flows.

Table 2. Survival table for selected winter-run and fall-run smolt release groups from the Livingston Stone Hatchery and Coleman Hatchery during critical drought years 2009, 2044, 2015 and normal year 2016.

Figure 2. Broodyear index for juvenile fall-run salmon catch in the lower Sacramento River at Knights Landing rotary screw trap 2008-2023. Source

Figure 3. Water temperature and streamflow in the lower Sacramento River at Wilkins Slough in March-April 2021. Red outline is period of (upstream) Coleman Hatchery smolt releases.

Figure 4. Tisdale screw trap collections of winter-run smolts in the lower Sacramento River in fall-winter of water year 2021. Source

Figure 5. Water temperatures in the lower Sacramento River at Wilkins Slough and Freeport during adult salmon immigration period in 2023. Green line represents safe level for adult migration. Yellow line is stress level and water quality standard. Red line is high stress and avoidance level.

October has just ended, and the spawning of spring-run Chinook salmon should be nearing completion.  The winter-run have already finished spawning, and their eggs are now hatching.  The fall-run salmon are in the rivers and beginning their spawning on the Hunter’s Moon.  The fall-run are often neglected after the two endangered runs are complete.  There are actions needed now to protect this biggest and most important run.  After all, the California Fish and Game Commission sacrificed the commercial and sport salmon fishing this year to let the fall-run recover from record lows.

The first signs of trouble in 2023 came with the the low number of returning Central Valley spring-run Chinook Salmon this year.  The decline was indicative of a sudden drastic collapse in all the salmon runs around the Central Valley.

In the northern Sacramento Valley, there are the Clear Creek and Battle Creek spring-run populations.  In the middle Sacramento Valley, there are the Mill and Deer Creeks populations with their remnant counterparts in nearby Big Chico and Antelope Creeks.  There is also the relatively robust (until 2023) Butte Creek population.  Then there is the Feather-Yuba population in the lower Sacramento Valley.  Finally, there is the new population being restored in the upper San Joaquin River near Fresno.  An October 11, 2023 joint news release from NMFS and CDFW describes the numbers of returning spring-run this year as drastically low, to the point that fishery agencies have begun capturing the wild yearlings still residing in the spawning creeks and transporting them to a UC Davis conservation hatchery to preserve the species.

An immediate need is to focus attention on the fall-run Chinook that normally pour into the rivers and begin spawning with the Hunter’s Moon.  Water year 2023 was a wet year, and salmon fishing has been closed in anticipation of predicted low numbers in this year’s spawning run.  It turns out drought years 2021 and 2022 had worse-than-predicted effects on the Valley salmon.

The news release from NMFS and CDFW says, “While other year-classes (or cohorts) will return in coming years, the 2019-2022 drought impacted multiple cohorts, increasing risks for extirpation.”  Actually, 2019 was a wet year and 2020 was a below-normal water year.  It is brood-years 2020, 2021, 2022, and now 2023, that the 2021-2022 drought damaged from many different directions.  Looking ahead, there is a bad forecast for the coming years.  Poor brood years 2020-2023 will lead to poor brood years in 2024-2027, and so on, unless we pay attention now to this year’s fall run.

The Actions Needed Now – Starting the First of November:

1. An intensive monitoring program to assess the damage.

2. Remaining wild and hatchery salmon need maximum protection – this includes a temporary conservation hatchery.

3. This year’s production, no matter how minuscule, must be protected. A substantial portion of the juveniles should be rescued and preserved.  If water year 2024 turns dry this winter, fry, fingerling, and pre-smolt salmon from all races should be captured and eventually transported to the Bay unless significant strategic, coordinated flow pulses can be provided or occur naturally.

4. All hatchery smolts should have at least an adipose fin-clip mark. As many as possible should be released to the Bay or coast for maximum survival.  The marks will be important to differentiate between hatchery and natural-born salmon in the coming years.

5. At locations where migrating adult spring-run salmon potentially originating from Clear, Battle, Mill, Deer, and Butte creeks are clearly stuck or off-course during fall-winter-spring of water year 2024, and where it is possible to collect them, fish agencies should attempt to capture them and return them to their natal stream or to the conservation hatchery. Locations include weirs, dams, ladders, or traps, as well as hatcheries.  This will require Genetic Stock Identification (GSI).

6. Juvenile salmon salvaged at south Delta export facilities this winter and spring should be handled as follows: pre-smolt and smolt salmon should be transported to Golden Gate pens for release. Salvaged fry and fingerlings should be hatchery reared or pen reared to smolt size for eventual pen release at the Golden Gate.

7. The fish agencies and water managers must provide prescribed streamflows and water temperatures in spawning streams and in rearing and migratory reaches. They should not even consider Temporary Urgency Change Petitions for water supply.  Given the current storage in reservoirs across the state, they should prioritize fall and winter flows for salmon over reservoir storage.

8. Fall-run salmon hatcheries will be short of eggs this year. Some hatcheries may need to ship eggs to other hatcheries.  The American River Fish Hatchery in the past sorted adult strays from the Coleman Hatchery on Battle Creek and transported their eggs back to Coleman.

9. Hatcheries should increase the proportion of smolt production trucked to the Bay or coast, where survival rates are up to ten times higher than river releases.

Site-Specific Actions:

10. Yuba River – In the lower Yuba River downstream from Englebright Dam to Marysville streamflow should be immediately increased for spawning and incubation.  Target minimum streamflow should be at least 700 cfs from Englebright Dam to Marysville gage – through spring.

Figure 1. New Bullards Bar Reservoir has never been fuller at this time of year.

11. American River – Water temperatures should be lowered to 55^oF to protect spawning salmon in this fall’s spawning season. This will require greater power bypass releases from the reservoir as begun in mid-October (Figure 2).  Folsom Reservoir is also “full.”

12. Upper Sacramento River – Streamflow should be maintained at a minimum of 7000 cfs (Figure 3) through the fall-winter-spring at Bend Bridge gage to provide good spawning, rearing, and emigrating conditions for salmon. Shasta Reservoir is also “full.”

13. Deer and Mill creeks – Streamflow from February through May should be maintained at a minimum of 100 cfs or higher to provide a clear migration corridor with water temperatures in the optimal range. Diversions should be disallowed when flows drop below 100 cfs in these months.

14. Butte Creek – Streamflow from February through May should be maintained to conform with the recommendations in the 2017 Draft Instream Flow Regime Recommendations Butte Creek.

15. Lower river migration corridors to and through the Delta – Water temperatures in winter and spring should be maintained below 60-65^oF (see Figure 4), the lower the better. Striped bass still eat a lot of salmon at 65^o

In conclusion, it is time for action.

Figure 2. Water temperature in the lower American River at Watt Ave gage in September-October 2023 and 6-year average. Water temperatures need to be 55F by November 1. They should have been no higher than 60F in October.

Figure 3. Streamflow in the upper Sacramento River at Bend Bridge gage in September-October 2023 and 59-year average. Flows should be maintained near 7000 cfs through the fall.

Figure 4. Water temperatures in spawning areas should be below 55^oF, while rearing and migration corridors should be below 60^oF through spring. Spawning reaches include Feather River at Gridley (GRL), Sacramento River from Keswick Dam (KWK) to Bend (BND), Stanislaus River at Ripon (RPN), American River at Watt Bridge (AWB), and Clear Creek at IGO (IGO). Migration and rearing corridors include lower San Joaquin River at Mossdale (MSD), upper Sacramento River at Red Bluff (RDB), lower Sacramento River at Wilkins Slough (WLK) and Freeport (FPT). Blue dotted line is spawning temperature limit. Red dotted line is rearing and migration limit.

It is early October 2023, and the fall-run salmon are running.  The California Department of Fish and Wildlife expects to open the ladder to the American River Hatchery on or about November 1.  There are already salmon in the lower American River from its mouth all the way to Nimbus Dam.

The run expected this year has a mixed forecast.  There was no ocean or river salmon fishery this year because of poor runs in the Central Valley during the 2020-2022 drought.  The fact that fishing was not allowed will improve the 2023 run size (escapement).  The 2020 run (parents of this year’s run) was pretty good (Figure 1).  But when brood year 2023 was rearing and migrating to the ocean, it was a critical drought year 2021, conditions under which juvenile salmon almost always have poor success in making the journey from rivers to the ocean.

Conditions in 2023 have been a mixed bag for the migration of adult spawners from the Bay to Central Valley rivers.  Summer 2023 started with warm water and low flows.  That changed when the Fall X2 requirement kicked in September (Figure 2).  The September Fall X2 flow pulse helped cool the lower Sacramento River and the Bay-Delta (Figure 3), and provided attraction flows for the adult salmon to move into the Bay and on toward the rivers.

An unforeseen problem has faced the running salmon when they hit the north Delta and mouth of the American River: water temperatures have been stressful for migrating adult salmon (>65^oF, Figure 4) despite high flows (3000 cfs) from the American River.  The water quality standard for the lower American River requires water temperatures to be maintained <65^oF in summer.  But water temperatures rose through September, with continuing increased water temperatures of water released from Folsom Reservoir (Figure 5).  Water year 2023 was a very wet year with above-average reservoir storage.  So why was the American River so warm?

The answer is that the powerhouse intakes at Folsom Dam had limited access to the cold-water pool, and the supply of accessible cold water was running short.  To ensure colder water for the hatchery and river for the November spawn, the Bureau of Reclamation began operating the powerhouse intakes in September to draw warmer water from the surface layers of the reservoir as the reservoir slowly drained.

The water temperature for spawning needs to be below 56^oF.  Getting the temperature down that low by November is a tall order, but it was achieved in the 2020-2022 drought (Figure 6) under much lower reservoir storage levels (the present level is 135% of average for October and is much higher than in 2020-2022).  Reclamation achieved November spawning temperatures in those drier, lower-storage years by releasing substantial cold-water from the lower dam outlets, bypassing the power intakes.   The power bypass measure will likely be needed again in 2023 to meet the November temperature targets in the river.

There is a case to be made that Reclamation should also have used the power bypass in September 2023 to maintain 65^oF at the Watt Avenue bridge.  Reclamation’s reluctance to use the power bypass to maintain release water temperature requirements further highlights the need for Reclamation to complete the planned refinements to the Folsom powerhouse intake system that will allow both continuous power generation and greater access to Folsom’s cold-water pool.

How else could this series of events have been avoided or at least improved?

First, summer flows in the lower Sacramento River should have been higher to help keep water temperatures at or closer to the standard of 68^oF (see Figure 3) at the Wilkins Slough gage, located  on the lower Sacramento River upstream of the mouths of the Feather and American rivers.  Flows at Wilkins Slough for wet year 2023 were well below the average for water years 1994-2003, when salmon did relatively well (Figure 7).  These low flows in 2023 contributed to poor conditions in the lower Sacramento River, the Delta, and the Bay.

Second, the water temperature in the  lower American River at the Watt Avenue Bridge (AWB) should have met the water quality standard of 65^oF until September, and should be kept below 60^oF in October (Figure 8).  After November 1, Reclamation should maintain temperatures below 56^oF for spawning.

Such improved conditions would improve the health of adult salmon spawning in the American River and its hatchery, as well as in other rivers and streams in the Sacramento River watershed.

Figure 1. Escapement (run size) for in-river spawning fall-run salmon in the lower American river 1952-2022.

Figure 2: Flow and water temperature at the Rio Vista Bridge July 15 – September 30, 2023.

Figure 3. Air and water temperature on the Sacramento River at Red Bluff (River Mile – RM – 240), and water temperature at Wilkins Slough (RM 120), Freeport (RM 50), and Rio Vista Bridge (RM 25). Also shown is water temperature standard at Red Bluff and Wilkins Slough.

Figure 4. Water temperature in the upper Sacramento River below Keswick Dam (RM 300), lower American River at Watt Avenue Bridge (AWB), the lower Feather River at Gridley gage (GRL), the lower Sacramento River at Wilkins Slough (WLK, RM 120) upstream of the Feather and American Rivers, and Freeport (FPT, RM 46) downstream of the American River.

Figure 5. Daily average water temperatures in the lower American River 9/10-10/3 2023 below Folsom Dam (AFD), at Fair Oaks gage below Nimbus Dam (AFO), at William Pond gage (AWP), and at Watt Avenue Bridge gage (AWB). The water quality standard in all water year types is 65oF maximum (year-round) at AWB.

Figure 6. September through December daily average water temperatures of Folsom Dam releases 2020-2022. Note the sharp drops in water temperatures in middle October from Power Bypass cold-water releases to provide target spawning temperatures (56^oF).

Figure 7. Average daily flows in the lower Sacramento River at Wilkins Slough, upstream of the mouths of the American and Feather rivers in 2023, compared to the average during the decade of strong escapement 1994-2003.

Figure 8. Water temperatures in the lower American River at Fair Oaks (below Nimbus Dam) June-September 2023 with average from prior eight years that included 5 critical dry years.