“Improbable Comeback” Not Looking Probable

In an April 19, 2020 blog post entitled Science of an underdog: the improbable comeback of spring-run Chinook salmon in the San Joaquin River, a UC Davis team describes the efforts over the past five years to recover spring-run Chinook salmon in the San Joaquin as a “good comeback story.” It is a great story – as far as it goes.  Eighteen years of litigation and fifteen years of restoration work have put water back in a river that Friant Dam completely dried up in 1950.  There are also some spring-run salmon in the river, and a few made it from near Fresno to the ocean and back in the last few years.

The goal of the reintroduction program is the long-term maintenance of a population of 30,000 spawning adults with negligible hatchery influence.  The count for the 2019 run was 23.  Reaching the goal is highly improbable in the present scheme of things.

Why?  As the UC Davis team stated:  “Most of the tagged fish that enter the interior Delta simply don’t make it out.”  Juvenile salmon from natural spawning areas and hatcheries do not survive downstream passage downstream to and through the Delta in necessary numbers to make the goal achievable.  There are simply too many “obstacles.”

The UC Davis team also stated:  “It is notably sad and ironic perhaps, that the quality of habitat in the lower river is so poor that the best migration path for salmon appears to be as a salvaged fish, trucked around the Delta by DWR or BOR staff.”  The word “best” is just the wrong word to describe a path and procedure that is founded on a dysfunctional fish salvage system that at its best saves a tiny fraction of the fish that the Delta pumps pull off course and ultimately decimate.  Returns of adult salmon to the San Joaquin River are extremely low (Figure 1).  Department of Water Resources and Bureau of Reclamation “staff” collect and truck these totally misdirected, stressed, and abused fish, and dump them into the waiting mouths of predators in the west Delta, not even bothering to truck salvaged fish to the Bay.  Compared to Sacramento River hatchery smolts, the odds of San Joaquin hatchery smolts being “salvaged” are one to two orders of magnitude higher (Table 1).

What could help recover San Joaquin River spring-run salmon?

  1. Reduce exports from the south Delta, especially from March through May.
  2. Increase San Joaquin River and tributary flows during adult and juvenile migration seasons.
  3. Improve habitat in spawning, rearing, and migration corridors from spawning reaches to the Bay.
  4. Capture wild juvenile spring-run below spawning reaches and transport them to the Bay.
  5. Transport hatchery and wild smolts via barge or floating net pens from lower rivers to the Bay.

So far minimal progress has been made on measures 1-3.  As yet, there has been no attempt to address measures 4 and 5 other than pilot studies (encouraging) by the Mokelumne River Fish Hatchery.

“Ironic” is also the wrong word to describe how Delta salvage operations are the least impossible longshot for San Joaquin smolts: it is absolutely infuriating that thirty years of dedicated and talented legal, biological and in-river effort can be undone by the Delta operations that DWR and BOR have just made more efficient at fish killing.

TABLE 1.  Comparison of “loss” in Delta salvage facilities between San Joaquin hatchery spring-run smolts and other Central Valley salmon hatchery smolts 2016-2020.  Note the word “loss” is used instead of “salvaged” in these tallies.  Source:  http://www.cbr.washington.edu/sacramento/tmp/deltacwttable_1587318641_393.htmlTABLE 1. Comparison of “loss” in Delta salvage facilities between San Joaquin hatchery spring-run smolts and other Central Valley salmon hatchery smolts 2016-2020. Note the word “loss” is used instead of “salvaged” in these tallies Table 1. Continued. Table 1. Continued.

Figure 1. Hatchery tag adult returns from San Joaquin releases in 2016 (dry San Joaquin water year). Green dots are San Joaquin hatchery spring run released above Merced River in San Joaquin. Blue dots are releases from Merced hatchery fall run released to the Delta near Sherman Island. Orange dots are Mokelumne hatchery fall run released to the Delta near Sherman Island unless specified: GGB = Golden Gate Bridge, HMB = Half Moon Bay on coast, R = Mokelumne River. Data source: https://www.rmpc.org

Follow-up on Spring 2020 Sacramento River Conditions

In a recent post (May 6, 2020), I discussed the need to increase flows in the lower Sacramento River to reduce water temperatures for emigrating juvenile spring-run and fall-run hatchery and wild Chinook salmon. I recommended maintaining water temperatures below 65°F/18°C per the scientific literature. Water managers increased flows (or reduced diversions) on about May 11 (Figure 1), and with the help of cooler weather (Figure 2), water temperatures came down significantly through the lower Sacramento River (Figures 1, 3, and 4).

The National Marine Fisheries Service (NMFS), California Department of Fish and Wildlife (CDFW), and US Bureau of Reclamation (BOR) have begun a multi-year study to evaluate the potential survival benefits for juvenile spring-run and fall-run Chinook salmon of managed spring flow pulses in the Sacramento River.1 Such action is prescribed in the NMFS 2019 biological opinion for the federal Central Valley Project. The problem with the prescription is that it applies only in wetter years when there is high Shasta Reservoir storage (4 million acre-ft end-of-April), while the need is greatest in drier years when reservoirs capture most if not all the water from limited precipitation events.

But why study the concept with 50 years or more of data available? Just looking at this spring’s data shows the role flow can play in keeping temperature below levels that are known to increase salmon mortality. In this blog I have shown over and over the order-of-magnitude benefits to population recruitment that comes from maintaining flows and water temperature. The scientific literature is replete with analyses of the effects of water temperature on salmon. We know that temperatures in the lower Sacramento River on May 9-10 were bad for immigrating adult salmon and emigrating juvenile salmon, so why not acknowledge the problem and correct it?

And why just study the benefit of a single flow pulse? Results would depend on so many factors. In Figure 1, weather forecasts indicated the May 7-9 heat wave days ahead, so why wasn’t the flow pulse applied earlier? Or were water managers simply responding to water demands or violations in water quality standards that occurred May 8-10 at Verona?

In any case, the May 2020 example shows that flows and water temperatures in the lower Sacramento River need to be actively managed to protect salmon.

Figure 1. Water temperature and streamflow in the Sacramento River at Wilkins Slough and Verona May 1-15, 2020. See Figure 4 for gage location.

Figure 2. Air temperature at Hood near Freeport May 1-15, 2020.

Figure 3. Freeport gage water temperature and daily average flow (tidally filtered) May 1-15, 2020. Figure 4 for gage location.

Figure 4. Gage stations in lower Sacramento River


  1. A link to the draft study plan: https://1drv.ms/b/s!ArkjAKW4WdKRwCWsW3cnyJdS5Zac

Klamath’s Scott River Salmon and Steelhead in Trouble

Scott River – April 2020

The Scott River is a major contributor to Klamath River salmon and steelhead runs.1 The fry of fall-run Chinook and Coho salmon that spawned in the Scott system this past fall-winter are now leaving their gravel beds. Steelhead are completing their spawning run. These salmon and steelhead are in for a tough year because flows are low (Figure 1), precipitation has been minimal (Figure 2), and the snowpack is well below average (Figure 3).

The state of California needs to step up to protect these iconic and socio-economically important wild salmon and steelhead runs and the critical habitats that support them. The State Water Resources Control Board, supported by the California Department of Fish and Wildlife, needs to maintain adequate flows in the Scott River through the fall. If the state does nothing, the river will dry up by summer, and most of the young fish will die.

The State Water Board and CDFW must control and carefully monitor surface diversions and groundwater extractions for pasture and hay irrigation. Otherwise, the river and all its aquatic life will die, and domestic-use water will dry up.

Coho salmon are a state and federally listed endangered species protected by law. Water rights issued and managed by the State Water Board require protection of these natural resources. Fish habitat is protected by state laws; state agencies need to enforce these laws. Local entities such as water districts, resource conservation districts, water and land trusts, tribes, communities, and landowners need to pitch in.

Figure 1. Streamflow in the Scott River September 2019 to April 2020, plotted next to 70-year average (log scale).

Figure 2. Monthly average precipitation in inches at Callahan, CA over past two decades. Note near zero precipitation in Feb 2020. Source: CDEC.

Figure 3. Snow survey data summary for Scott River and Shasta River watersheds in 2020. Source: CDEC.

Spring 2020 Sacramento River Conditions and Hatchery Releases

Federal and state hatcheries are feeding striped bass with juvenile salmon in the Sacramento River and Delta yet again this spring.  As of April 22, 2020, hatcheries have released over 16 million salmon smolts into the Sacramento River system (Table 1).  While about two-thirds of these releases so far took place under relatively good conditions (moderate flows, flow pulses, and cool water through early April), the latest one-third have been released under increasingly lower flows and high, stressful water temperatures (Figures 1 and 2) that lead to high rates of predation.  Hatchery smolts lingering from the earlier releases are also subjected to these conditions.  Millions of wild smolts are also at risk, as they too have been emigrating with the early April flow pulse (Figure 3).

In addition to predatory fish like striped bass, another predaor also lurks in the south Delta: the federal and state export pumps (Figures 4 and 5).

With millions more hatchery smolts and wild emigrants to come through early June, the prognosis for future adult returns from these fish looks grim unless some effort is exerted by water agencies to increase river flows and Delta inflow/outflow in the coming weeks.  Future hatchery releases this spring should be transported to the Bay.  Flow pulses are needed, but those prescribed in the new federal biological opinion are only required in wetter years.  Flows in the Sacramento River at a minimum should be above 5000 cfs at Wilkins Slough and above 10,000 cfs at Freeport.  Water temperatures should be maintained below 18°C/65°F to give emigrating salmon a chance to survive.

Table 1.  Major Sacramento River hatchery smolt releases in spring 2020.

Figure 1. Flow and water temperature in the lower Sacramento River at Wilkins Slough spring 2020. Yellow lines denote major hatchery smolt releases into the upper river.

Figure 2. Flow and water temperature in the lower Sacramento River at Freeport in the north Delta spring 2020. Yellow lines denote major hatchery smolt releases into the upper Sacramento River. Magenta lines denote major hatchery smolt releases into the Feather River.

Figure 3. Salmon smolt survey collections of unmarked juvenile hatchery and wild salmon in 2020. Magenta circle outline winter fry movement. Green circles denote spring smolt movement. Note movement peaks coincident with flow pulses.

Figure 4. Salvage of unmarked juvenile hatchery and wild salmon at south Delta export facilities in water year 2019-2020.

Figure 5. Salvage of unmarked juvenile hatchery and wild salmon at south Delta export facilities in water year 2019-2020.

Adult Winter-Run Salmon Migration in Jeopardy under New Biological Opinion

As we enter May 2020, winter-run Chinook salmon are in the middle period of their near 300-mile adult migration up the Sacramento River to spawning grounds below Shasta Dam near Redding, CA. These adult salmon are in jeopardy this spring from low flows and high water temperatures in the lower Sacramento River. The new federal biological opinion on the long term operation (BO-LTO) of federal Central Valley Project (CVP) and State Water Project (SWP) that went into effect in October 2019 is not protecting these migrating adult winter-run.

State of California water right permits for the CVP/SWP and the Central Valley Basin Plan have prescribed standards (e.g., maximum allowed lower Sacramento River temperature of 68°F). However, federal and state agencies have largely ignored these standards.1

Figures 1-4 depict the basic problem: water temperatures in the lower 120 miles of the Sacramento River from Wilkins Slough downstream to Rio Vista are in excess of stressful or near-lethal levels, levels known to hinder or even block migrations, and levels known to reduce (1) survival, (2) successful spawning, and (3) subsequent egg viability of the adult salmon.

At a minimum, water temperature objectives in the Basin Plan and Water Right Order 90-05 should be met. It is simply unacceptable for water temperatures at Verona (RM 80) to be 70°F or higher. Maintaining lower river flows near 6000 cfs near Wilkins Slough (RM 120) and near 10,000 cfs near Verona (below the mouth of the Feather River) is necessary to meet temperature objectives. Such levels would also reduce water temperatures downstream in the Delta (Freeport and Rio Vista). The 68°F objective in the Basin Plan is a year-round standard and requirement of the water right permit for the state and federal water projects in the Sacramento River Basin.

The 68°F objective was met more frequently in recent below normal water years 2012, 2016, and 2018, at least well into the month of May (Figure 5). It was also met more frequently later into the spring in the 2008-2010 drought period (Figure 6).

In conclusion, there is a continuing eroding of the Sacramento River temperature standard, which appears to have accelerated under the new BO-LTO. Higher spring water temperatures are a serious risk to the winter-run salmon population.

Figure 1. April 2020 Sacramento River water temperatures near Red Bluff (RDB, RM 240), Wilkins Slough (WLK, RM 120), and Verona (VON, RM 80). Blue line is upper limit of optimal migration temperature. Green line is safe limit. Orange line is beginning of stressful level. Red line is beginning of lethal or avoidance/blockage level.

Figure 2. April 2020 Sacramento River water temperature and flow near Wilkins Slough (WLK, RM 120). 20°C is equivalent to 68°F.

Figure 3. April 2020 Sacramento River water temperatures and tidally filtered flow near Freeport in the Delta.

Figure 4. April 2020 Sacramento River water temperatures and tidally filtered flow near Rio Vista in the Delta.

Figure 5. Spring water temperatures in the lower Sacramento River at Wilkins Slough (WLK) and Verona (VON) in 2012, 2016, and 2018 below-normal water years. Red line is Basin Plan maximum objective.

Figure 6. Spring water temperatures in the lower Sacramento River at Verona (VON) in 2008, 2009, and 2010. Red line is Basin Plan maximum objective.


  1. The BO includes this statement on page 230: “The Spring pulses are also expected to benefit adult winter-run Chinook salmon migrating up the Sacramento River later in the spring. The spring pulses would provide improved water flows that in turn provide cooler temperatures (improved Water Temperature), and allow for better passage conditions”. However, the BO-LTO prescribes no spring flow pulses at all for drier years like 2020.