Category Archives: Water Quality

The 18 May Storm Brought Water and Fish to the Bay

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A mid-May storm in the northern Central Valley brought approximately 250,000 acre-ft of new water to the Sacramento River watershed. A rough conservative estimate indicates approximately 150,000 acre-ft of the storm’s water was put into storage in northern Valley reservoirs, while roughly 100,000 acre-ft of the storm’s water reached the Delta and Bay. No noticeable effect from the storm was observable in the southern Valley or San Joaquin River.

Shasta Reservoir storage at the northern end of the Valley increased 80,000-100,000 acre-ft from the storm (Figure 1). About 50,000 acre-ft of runoff was stored directly in Shasta Reservoir. Another 50,000 acre-ft was added to Shasta storage by reducing downstream releases because downstream irrigation demands were being met by tributary inputs from the storm (Figure 2).

Local runoff and tributary inputs from the storm in the Redding and Red Bluff area increased streamflow in the lower Sacramento River. Sacramento River flow in the area as measured at the Bend Bridge Gage (BND) increased 3000-4000 cfs (about 30%) on May 18-19 (Figure 3). The lower river flow pulse passed downstream by Colusa (RM 144) and Wilkins Slough (RM 120) on May 20-22, and Verona (RM 70) and Freeport (RM 35) on May 21-23 (Figure 3). Most of the storm’s runoff that did enter the lower Sacramento River, other than the 3000-5000 cfs diverted for irrigation, eventually reached the Bay, doubling Delta outflow to the Bay (Figure 4). This significant flow pulse helped young salmon and steelhead passing through the Delta to reach the Bay (Figure 5) and reduced the loss of the young salmon and steelhead at the Delta export pumps (Figure 6). The flow pulse helped keep water temperature down to safe limits (<68°F) (Figure 7). However, after the pulse passed and flows dropped, water temperatures reached 74-77°F, near or at the lethal level for salmon, prompting what appears to be an “emergency” increase in reservoir releases in late May to alleviate water quality and permit violations of water temperature standards.

Most of the lower river flow pulse reached the Bay because Delta exports were not increased as would have been allowed by the latest National Marine Fisheries Service’s (NMFS) 2019 Biological Opinion (BO) for the long-term operations of the Central Valley Project (CVP) and State Water Project (SWP). On May 11, 2020, Judge Dale A. Drozd of the U.S. District Court for Eastern California issued a preliminary injunction sought by the state of California and several environmental and fishing groups. The injunction prevented the Bureau of Reclamation from implementing the new BO until at least June 1, 2020. One immediate result of the injunction was that NMFS’s 2009 BO was put back into effect, with restrictions on May exports.

If there had been no 2009 BO restrictions on Delta exports (the 2009 BO limited exports to 100% of San Joaquin River inflow to the Delta), south Delta exports could have been 6000 cfs (under a State Water Board limit of 35% of total Delta inflow) instead of 1000-2000 cfs (Figure 8). Such higher exports would have greatly reduced the added beneficial Delta outflow from the storm and would have had a greater impact to emigrating salmon and steelhead smolts from the Sacramento River and the San Joaquin River. Less Delta outflow would also have limited benefits to endangered longfin and Delta smelt in the Bay.

In conclusion, the total amount of water from the northern California storm was near 75,000 acre-ft in the Redding-Shasta watershed, with about a third captured in Shasta Reservoir, a third going to irrigation deliveries instead in lieu of deliveries from Shasta storage, and a third passing downstream to the Delta and Bay. The judge’s decision to allow approximately 40% of the stormwater to reach the Bay, at least temporarily, has helped sustain salmon and smelt in this otherwise dry year. After the flow pulse, slow-to-react water managers allowed water temperatures to spike, threatening the listed salmon and smelt that remained in the rivers and the Delta.

Figure 1. Shasta Reservoir storage May 2020. Red line indicates projected storage before the mid-May storm. The difference between the two lines is a rough estimate of added new storage.

Figure 2. Shasta/Keswick dam releases in May 2020. The cuts in Shasta/Keswick releases in mid-May correspond to increase in downstream stormwater inputs that reduced demands on Shasta storage.

Figure 3. Sacramento River streamflow in May 2020 as measured at Bend (RM 259), Hamilton City (RM 200), Colusa (RM 144), Wilkins Slough (RM 120), Verona (RM 70), and Freeport (RM 35). The difference in flows at Bend and flows at Hamilton City, Colusa, and Wilkins Slough in early May is due to irrigation diversions downstream of Bend. Increased flows at Freeport and Verona compared to flows at Wilkins Slough are due to Feather River and American River inputs. Source: http://www.cbr.washington.edu/sacramento/data/ .

Figure 4. Delta outflow (DTO), and Sacramento River flow at Freeport (FPT, RM-35), Verona (VON, RM-70), and Wilkins Slough (WLK, RM-120) in May 2020.

Figure 5. Unmarked salmon smolts captured in trawls leaving the Delta at Chipps Island in eastern San Francisco Bay, 8/1/2019 to 5/15/2020. Note increase in smolts escaping to the Bay after May 11.

Figure 6. Unmarked juvenile salmon salvage at south Delta export facilities 10/1/2019-5/18/2020. Delta exports are shown in acre-ft in center panel. Note reduced salvage when exports were at minimum levels (about 3000 acre-ft per day, or about 1500 cfs) after mid-May.

Figure 7. Sacramento River flow and water temperature at Freeport (FPT, RM-35), Verona (VON, RM-70), and Wilkins Slough (WLK, RM-120) in May 2020. Note the excessively high water temperatures (lethal for salmon at Verona, otherwise highly stressful) at Verona and Wilkins Slough in late May.

Figure 8. May 2020 Delta exports from federal Tracy Pumping Plant (TRP) and state Harvey Banks Plant (HRO).

 

“Improbable Comeback” Not Looking Probable

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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

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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

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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.

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

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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. ↩