Category Archives: Chinook Salmon

Partnership Shares Science to Find Fish and Water Solutions

Posted on by

“This month six California and federal agencies representing water management, fish, and wildlife, along with the Sacramento River Settlement Contractors, signed onto the Sacramento River Science Partnership. The Partnership establishes an interagency science collaborative in which members will develop, share and discuss science to inform water management activities and protection of fish in the mainstem Sacramento River.” (8/25/20 News Release)

  •  The seven signatories will foster and advance science to inform sustainable solutions to water management challenges including conflicts between water supply delivery and fish survival.

The time when anyone thought that the problems confronting Central Valley salmon could be solved with more science is long gone. The problems and solutions have not really changed in the 40+ years I have been involved. And the problems are only getting worse. Why is it so hard to address them?

The Problems

As a consequence of rainfall, snowmelt, reservoir storage and release, and water diversions, flows in the Sacramento River, have become so low and erratic that they strand salmon spawning redds and create prolonged high water temperatures in the juvenile rearing and migration reaches of salmon. It is a wonder that there are any wild salmon left. Without hatcheries, there would be few if any salmon in the Central Valley at all.

Spring-Summer Water Temperatures

Spring-summer water temperatures in the lower Sacramento River are bad. They kill salmon and sturgeon, block migrations, lead to poor juvenile salmon growth, early migration, high predation, and cause huge predation problems for young hatchery and wild salmon. The high temperatures exceed state water quality standards and water project permit requirements. Yes, water temperatures were bad during the 2013-2015 critical drought, as might be expected (Figure 1). But they have also been bad in the five normal and wet years (2016-2020) since the drought (Figure 2). The safe level is 65°F, but the standard is set at 68°F, above which stress and higher mortality occurs. 68° is supposed to be an upper limit that should not be exceeded, and in past decades it rarely was. It is now the accepted norm, and even then it is not enforced.

In 2020 (Figure 3) spring water temperatures were detrimental to the upstream migration of endangered winter-run and spring-run salmon, emigrating juvenile fall-run salmon, and larval and juvenile sturgeon. High summer temperatures hinder migration of adult fall-run salmon and are detrimental to survival of winter-run fry, over-summering late-fall-run and fall-run salmon smolts, and rearing juvenile sturgeon.

Fall Drops in Water Levels

Often, usually in October-November, flow releases from Shasta reservoir drop sharply in response to decreasing downstream irrigation demands. The decreases lead to fall-run salmon redd dewatering in the upper river spawning area near Redding and poor habitat and emigration flows for winter-run and late-fall run juvenile salmon.

Stranding

Adult and juvenile salmon are stranded throughout the Sacramento River floodplain after winter-spring, high-flow events. In addition, drops in water surface elevation of four feet in the fall (Figures 4 and 5), soon after spawning de-water the vast majority of fall-run spawning redds in the 20-mile spawning reach downstream of Keswick Dam. Drops in flows after floodway weir spills (Figures 6 and 7) strand adult salmon and sturgeon that are migrating upstream, and also strand juvenile downstream emigrants in the Sutter and Yolo floodway bypasses.

Hatchery Releases

Releases of millions of hatchery-raised salmon and steelhead smolts in winter and spring into the lower Sacramento River from federal and state hatcheries compromise wild salmon and steelhead fry, fingerling, and smolt survival throughout the lower Sacramento River. Hatchery salmon and steelhead prey upon and compete with wild salmon and steelhead, and attract non-native predatory striped bass that also feed on wild salmon and steelhead.

Solutions

A new science plan for the upper reaches of the lower Sacramento River is not going to solve the problems that stem from failure to act on what science has told us for decades.

Solutions to the problems outlined above abound. These solutions are well documented in the Central Valley Salmon and Steelhead Recovery Plan (NMFS 2014) and other stakeholder plans.1 The most important solution, is water temperature limits in the lower Sacramento River, which were adopted decades ago in state water permits and water quality control plans. These limits designed to protect salmon are simply no longer enforced.

Figure 1. Water temperature in the lower Sacramento River from 2013-2015 critical drought years near Grimes, CA. Also shown is average for the past 11 years of record. https://nwis.waterdata.usgs.gov/nwis/

Figure 2. Water temperature in the lower Sacramento River from 2016-2020 post-drought years near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 3. Water temperature in the lower Sacramento River in 2020 near Grimes, CA. Also shown is average for the past 11 years of record.

Figure 4. Sacramento River flows in fall of 2013 below Keswick Dam near Redding.

Figure 5. Sacramento River water surface elevation in fall of 2013 below Keswick Dam.

Figure 6. Spills of water from Sacramento River over Tisdale flood control weir during the period from December 2013 to February 2015. Source: CDEC

Figure 7. Spills of water from Sacramento River over Tisdale flood control weir during the period from January 2016 to May 2017. Source: CDEC

Saving Native Central Valley Salmonids

Posted on by

No, the fish below is not a Central Valley salmon or trout. It is a Yellowstone Cutthroat Trout from the Yellowstone River in Yellowstone National Park. This iconic species is beginning to recover from competition and predation by non-native brook, brown, rainbow, and lake trout. Yellowstone Park over the past decade has carried out an intensive eradication program of the non-native salmonids to save the iconic native cutthroat. A similar program has been underway to save the Snake River Cutthroat on the South Fork of the Snake River from Grand Teton Park in Wyoming downstream into Idaho. The eradication programs include rotenone poisoning of tributaries, gill-netting (lake trout in Yellowstone Lake), and regulations requiring angler removal (rainbow trout).

Yellowstone Cutthroat Trout caught and released in the Yellowstone River in Yellowstone National Park summer 2018

California has excellent programs to protect some of its iconic trout and salmon through strict regulations and habitat protection and enhancement.

  • Redband Rainbow Trout in the upper McCloud River
  • Golden Trout in the upper Kern River
  • Lahontan cutthroat of the Truckee drainage.
  • Coastal cutthroat (NorthCoast streams)
  • Paiute cutthroat of the eastern Sierras.
  • Winter Run Chinook salmon (endangered) spawning grounds upstream of Redding are now closed to trout angling.
  • Spring Run Chinook Salmon (threatened) spawning tribs protected
  • Wild steelhead – no harvest in mark-selected fisheries (photo below)

Wild Rainbow Trout/Steelhead caught and released in the lower Yuba River near Marysville January 2019.

One survival bottleneck that needs opening for salmon and steelhead in the Central Valley is predation by non-native fish. There is a long list of non-native and native predators from which native fish need protection. The best protection is to minimize native-nonnative habitat interactions. That can best come from adequate physical-geographical habitat and habitat water quality for natives while minimizing non-native fish habitat. Changes are necessary because of global warming and continually increasing demands on water. Stream flows are too low, water temperatures are too high, waters are clearer, and in-stream cover is low, factors that all favor non-native predators and competitors.

Because many of the non-natives are sportfish with strong angler followings, non-lethal controls best serve to reduce overall predation effects on native fishes.

  • Provide natural spring flow pulses in rivers and tributary tailwaters to help emigrating salmonids avoid predators.
  • Keep water temperatures lower in rearing habitat and migrating routes of native fish.
  • Maintain the low salinity zone, the primary rearing area for native fishes, in the Bay downstream of the Delta.

At some point population controls on non-native fish may have to be considered despite their inherent problems and low potential for success.1 Note that despite the use of 50 miles of gill nets and removal of hundreds of thousands of pounds of lake trout each year in Yellowstone Lake, lake trout remain abundant. Predator control through removal would be far more difficult in the Central Valley and Bay-Delta.

Summary and Conclusion

I remain skeptical on how effective the individual actions can be, but a comprehensive multi-action program such as that employed for the Yellowstone Cutthroat Trout has some chance of success. Such a program would come with tough choices and require considerable resources, but may need to be part of saving Central Valley salmon and steelhead. Focus should be on increasing the amount of native fish habitat and bettering spawning, rearing, and migratory habitat conditions.

 

A Case for Better River Flows and Delta Outflow in June

Posted on by

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

Posted on by

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

Posted on by

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).