Category Archives: Fish (general)

Delta Smelt Sanctuary – Deepwater Ship Channel

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In a March 2020 post, I described where the remnants of the endangered Delta smelt population spawn and rear in the Sacramento Deepwater Ship Channel (Ship Channel) in the north Delta (Figure 1). In this post, I describe how the rearing conditions in the Ship Channel are poor. This can be seen by comparing habitat conditions in the Ship Channel with those in the lower Sacramento River channel at Freeport several miles to the east in late spring 2020.

Net Flow

Net flow (cfs) in the Ship Channel remains near zero, since the gate at the north end of the channel near Sacramento remains stuck in the closed position as it has been for several decades (Figure 2).

Water Temperature

Water temperature (oC) is significantly higher in the stagnant flows of the Ship Channel than at Freeport, often reaching into the lethal range 23-25°C for Delta smelt (Figure 3).

Salinity

Salinity (conductivity) is much higher in the Ship Channel because of discharges from urban sewage treatment plants and agricultural operations (Figure 4).

Turbidity

Turbidity is much higher in the Ship Channel due to higher plankton production and port-bound ship traffic in the relatively shallow and narrow Ship Channel (Figure 5).

Dissolved Oxygen

Dissolved oxygen levels are much lower in the Ship Channel because of warmer water, high concentrations of suspended organic sediments, and higher plankton production (Figure 6).

Interpretations and Conclusions

Delta smelt are attracted to the Sacramento Deepwater Ship Channel in winter and early spring to spawn in the relatively warm, low salinity, turbid, and more productive water. The adult smelt can also easily tidal-surf up the ship channel without having to content with strong downstream currents of the Sacramento River channel. Their eggs hatch early to an awaiting abundant plankton food supply. However, in spring the Ship Channel lacks net downstream flows to carry the young smelt to the Bay. By late spring, water temperatures in the Ship Channel reach lethal levels for the young smelt.

Opening the gate at the north end of the Ship Channel would help to alleviate the problems by providing net flow with cooler water temperatures, and by flushing and diluting the stagnant waste waters in the Ship Channel. An operable gate at the head of the Ship Channel would allow adaptive management of the habitat conditions for smelt.

Figure 1. Locations where Delta smelt young were captured in EDSM surveys in July 2019. Circles represent regions. Numbers are total July catch in region. The 94 represents the young smelt captured in the Deepwater Ship Channel.

Figure 2. Net daily flow (cfs) in the Ship Channel and in the Sacramento River at Freeport in June 2020. The green line shows flow in the Ship Channel.

Figure 3. Water temperature in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows the water temperature in the Ship Channel.

Figure 4. Conductivity (salinity) in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows salinity in the Ship Channel.

Figure 5. Turbidity in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows turbidity in the Ship Channel.

Figure 6. Dissolved oxygen in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows dissolved oxygen in the Ship Channel.

 

 

A Case for Better River Flows and Delta Outflow in June

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When the State Water Board gets around to finally updating decades-old Central Valley water quality standards, it should bring back some old spring standards, keep some good ones, and add some new ones to provide essential protection to salmon, steelhead, sturgeon, smelt, and many other native fish populations.  One focus should be on improving survival of wild spring-run and fall-run salmon smolts migrating from Central Valley spawning rivers to the Delta, Bay, and ocean.

With its high spring water temperatures (Figure 1), 2020 is a good example of a solvable problem.  The survival of wild spring-run and fall-run salmon smolts depends on sufficient flows and low water temperatures in the spring.  This natural selection process, once tied to the natural spring snowmelt cycle,  has been disrupted by reservoir storage and water diversions.  Wild smolt emigration peaks in spring and extends into early summer (Figure 2).  Sturrock et al. (2019) found that late spring smolt survival suffered from poor emigration habitat conditions.  This affects population diversity because of the disproportionate loss of wild smolts in the late spring.

June Delta Exports

June exports in recent wet years (2011, 2017, and 2019) have averaged 9000-11,000 cfs under the State’s current State D-1641 standards.  This is a new impact (since 1995) that has manifested itself in a decreased proportion of wild fish in the salmon runs, thus threatening the very integrity of the populations and commercial and sport fisheries.  Under the previous D-1485 standards, south Delta project exports in June were limited to 6000 cfs in all year types.

June River Flows and Water Temperatures

June river flows should be sustained to help move smolts downstream and maintain water temperatures below stressful levels (less than 68°F/20°C).  River flows need to be adequate to keep water temperatures in the lower sections of the Sacramento River below 68°F/20°C, as recognized in the Central Valley Basin Plan’s water quality standard.  The flows needed to maintain water temperatures depend on air temperatures.  Over the past decade, water temperatures have exceeded the target in June in the lower Sacramento River even in wet years 2011, 2017, and 2019 (Figures 3 and 4).

June Delta Inflow

June Delta inflows need to be of sufficient magnitude to help salmon smolts pass through the Delta in a timely fashion, and not get diverted off-course toward the south Delta export pumps or succumb to huge numbers of predator fishes.  June flow entering the north Delta at Freeport needs to be maintained near 20,000 cfs to maintain water temperatures near 68°F/20°C (Figure 5).

June Delta Outflow

With 20,000+ cfs inflow and south Delta exports limited to 6,000 cfs, Delta outflow will be 10,000+ cfs (the other 4,000 cfs is from within-Delta diversions).  This is sufficient to keep the Low Salinity Zone west of the Delta and salmon smolts moving toward the Bay and Ocean.

Summary

In conclusion, the present year-round water temperature standard for the lower Sacramento River, 68°F/20°C, should be sustained through June.  New State Board standards should limit south Delta exports in June to 6,000 cfs to protect wild salmon smolts that are emigrating from Central Valley rivers.

Figure 1. Water temperature in the Sacramento River in the north Delta in spring 2020, along with recent 22-year median daily average. Water temperatures above 68°F/20°C severely stress emigrating salmon smolts. Water temperatures above 75°F/24°C are lethal to salmon. Water temperatures above 70°F/21°C hinder or block the migration of adult winter-run and spring-run salmon as they move upstream in spring.

Figure 2. “Timing of ocean entry of fish released from the Feather River hatchery (blue) and wild out-migrating (red) from 2002 to 2010. The area of each violin represents the proportion of fish out-migrating at that Julian day and is normalized to the total abundance of outmigrants for that year. The black lines represent the interquartile range (first to third quantiles). Hatchery release data for the Feather River Hatchery (FRH) are from Huber and Carlson (2015). Data for ’wild’ (unmarked) fall-run sized outmigrants are from the USFWS Chipps Island Midwater Trawl.” Source: https://www.nrcresearchpress.com/doi/10.1139/cjfas-2017-0273#.XuY87C0idvJ

Figure 3. Sacramento River flow and water temperature at the Verona gage just downstream of the mouth of the Feather River, 2008-2017. July 1 for each year is equidistant between the vertical lines.

Figure 4. Sacramento River flow and water temperature at the Wilkins Slough gage upstream of the mouth of the Feather River, 2008-2020. July 1 is one-quarter and three-quarters distance between each of the two-year period vertical lines.

Figure 5. Sacramento River flow and water temperature at the Freeport gage in the north Delta downstream of the mouth of the American River, 2016-2020. June flows (immediately to left of July 1 lines) of 20,000 cfs maintain water temperatures near 20°C.

 

American River Salmon Shortchanged

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The American River fall-run Chinook salmon are often referred to as a hatchery run. They are confined to the lower 20 miles of river below Folsom-Nimbus dams and are supplemented by Nimbus Hatchery smolt releases. Adult escapement (run size) is estimated from hatchery counts (Figure 1) and in-river spawning surveys (Figure 2). The run peaked with 100,000+ spawners from 2000-2004, after six wet years (1995-2000) and the initiation of large-scale releases of hatchery smolts to the Bay beginning in 1995 (Figure 3). After the initial success of Bay releases, the total numbers of smolts released dropped from the 8-12 million range to 4-5 million around the year 2000.

Since 2010, more releases have been shifted back to the river. The shift seems appropriate in wetter years like 2010, 2011, 2017, and 2019, but not in drier years like 2012, 2013, 2016, and 2018.1 Adult returns from dry year releases have been 2-to-7 times higher for Bay releases than for river releases. In 2020, a dry year, releases to the river occurred in early May, when downstream water temperatures were above the 68°F/20°C stress limit for juvenile salmon (Figure 4).

Unless winter-spring flows and water temperatures in the American River and Delta are improved,2 and problems with water temperatures during the fall spawning season are fixed,3 wild and hatchery production from the American River will continue to suffer. Until these issues are resolved, continued releases of American River hatchery smolts to the Bay remain necessary to sustain the salmon run.

For more on the American River hatchery program, see http://goldenstatesalmon.org/2020-salmon-update/ and https://www.facebook.com/NimbusHatchery/videos/932316603863844/ .

Figure 1. Fall-run salmon in-river escapement estimates for the American River (1952-2018).

Figure 2. Fall-run salmon hatchery escapement estimates for the American River (1955-2018).

Figure 3. Nimbus Hatchery releases to the American River (in-stream) and to the Bay 1991-2019.

Figure 4. Sacramento River water temperature (degrees C) in the northern Delta downstream from the mouth of the American River, from mid-April to mid-May 2020.

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