“Improbable Comeback” Not Looking Probable

Posted on May 18, 2020 by Tom Cannon

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?

Reduce exports from the south Delta, especially from March through May.
Increase San Joaquin River and tributary flows during adult and juvenile migration seasons.
Improve habitat in spawning, rearing, and migration corridors from spawning reaches to the Bay.
Capture wild juvenile spring-run below spawning reaches and transport them to the Bay.
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.html 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 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

Posted on May 16, 2020 by Tom Cannon

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

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

Spring 2020 Sacramento River Conditions and Hatchery Releases

Posted on May 6, 2020 by Tom Cannon

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.

Franks Tract – Smelt Trap

Posted on April 28, 2020 by Tom Cannon

In a May 2019 post, I described the central Delta as a salmon trap for juvenile salmon. This post describes the “smelt trap.” Franks Tract in the central Delta (Figure 1) is a longfin and Delta smelt trap. Longfin smelt were vulnerable to the trap in March 2020 (Figures 2 and 3). Flow was reversed in False River (Figure 4) because of south Delta exports.

It’s not just the net flow that makes Franks Tract a smelt trap. It is also tidal pumping of 50,000 cfs in-and-out. What goes into Franks Tract on the flood tide does not come back out the same (Figures 5-9). It is different water, warmer, clearer, with less plankton, and probably less smelt larvae and juveniles. Smelt are simply tidally-pumped into the central Delta where they are susceptible to warmer, less turbid, predator-laden waters of Franks Tract and the central and south Delta. Most young smelt probably succumb before reaching the south Delta export pumps.

This is another reason why winter Delta exports need restrictions and why the Franks Tract restoration project with its tide gate on False River needs to proceed as part of the state’s program to recover longfin and Delta smelt. For more detail on the proposed project see: https://mavensnotebook.com/2019/02/07/bay-delta-science-conference-franks-tract-feasibility-study-applying-the-guidance-of-a-delta-renewed/ .

Figure 1. Franks Tract and False River gage location in west Delta.

Figure 2. Longfin smelt distribution in March 2020 20-mm Survey #1.

Figure 3. Longfin smelt distribution in March 2020 Larval Smelt Survey #6. Station 901 is in Franks Tract.

Figure 4. False River net daily tidally filtered flow (cfs) in March 2020.

Figure 5. Hourly flow at False River gage March 29 to April 5, 2020.

Figure 6. Hourly water temperature at False River gage March 29 to April 5, 2020.

Figure 7. Hourly turbidity at False River gage March 29 to April 5, 2020.

Figure 8. Hourly chloropyll at False River gage March 29 to April 5, 2020.

Figure 9. Hourly EC at False River gage March 29 to April 5, 2020. Note slightly brackish water (300-500 EC) moves upstream in False River on flood tides (Figure 5), but returns fresher on ebb tide from mixing in Franks Tract.

A Month of High Exports Pulls Salmon and Smelt to Delta Pumps

Posted on April 22, 2020 by Tom Cannon

Increased Delta exports by the federal Bureau of Reclamation in early April resulted in increased salvage of salmon and longfin smelt at the Central Valley Project’s south Delta Tracy Pumping Plant. Salmon smolts salvaged were predominately from the San Joaquin spring-run salmon recovery program hatchery (Figures 1 and 2). Longfin smelt salvage increased in mid-April (Figure 3) as young longfin reached salvageable size (~25 mm).

Salvage at the State Water Project was much lower in April as the California Department of Water Resources’ (DWR) reduced exports to try to offset the impacts of Reclamation’s increased pumping (Figures 2 and 3).

The state’s Bay-Delta Water Quality Control Plan requires that exports be reduced to be no higher than the San Joaquin River flow at Vernalis from April 15 through May 15. The Bureau of Reclamation and the California Department of Water Resources (DWR) were allowed to move those dates up in 2020, so that the month-long reduction began on April 10 (Figure 4). The average Vernalis flow was about 1500 cfs in mid-April, which is why exports wound down as required (Figure 3).

High exports in early April drew migrating salmon and longfin smelt into the south Delta. Old and Middle River (OMR) flows reached their limit of -5000 cfs (Figure 4). Thus, even after Reclamation and DWR reduced exports on April 10, salvage of both salmon and smelt continued to be high for a week, tapering down to lower levels on April 20.

State and federal exports should not have been ramped up in late March and early April. Had they been given the opportunity, the joint state and federal smelt and salmon science working groups would have recommended a range of -1500 to -2500 cfs OMR limit given the risks to salmon and smelt. However, in the epoch of the 2020 federal Biological Opinions for Delta operations, Reclamation has chosen to export as much as allowed by its view of the letter of the law. California’s view of the law is different: on April 21, 2020, California sought an injunction as part of its ongoing lawsuit against Reclamation’s operations under the new BiOps. See https://oag.ca.gov/system/files/attachments/press-docs/Memorandum%20in%20support%20of%20Preliminary%20Injunction.pdf and https://oag.ca.gov/system/files/attachments/press-docs/CNRA%20et%20al.%20v.%20Ross%20et%20al.%20FAC.pdf

If we want to save salmon and smelt, we simply must reduce exports in winter and spring, especially in drier years, as was generally standard procedure over the past decade under the 2008-09 federal Biological Opinions.