Author Archives: Tom Cannon

Saving Native Central Valley Salmonids

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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.

 

June 2020 Delta Outflow – New State Standard Needed

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I recommended a new June Delta outflow standard of 10,000 cfs in a post on June 23 2020. This increase from the current standard of 7000 cfs would keep salt and Delta smelt out of the Central Delta and better maintain adequate water temperatures for emigrating Central Valley salmon smolts.

In this post, I consider the recommended 10,000 cfs value in the context of how the California Department of Water Resources (DWR) and the Bureau of Reclamation (Reclamation) estimate Delta outflow as they manage Delta hydrology and federal and state exports from the south Delta. This should further explain why an increase in the June Delta outflow standard is necessary.

It helps to recall my description in a September 2019 post how DWR and Reclamation estimate Delta outflow: “Delta Total Outflow is a daily-average algorithm calculated in cubic feet per second (cfs) for Station DTO, a hypothetical location near Chipps Island in Suisun Bay.“ This is different from the US Geological Service’s (USGS) method of calculating real-time outflow. As an example, I overlaid the DWR and USGS for the summer of 2018 (Figure 1).

The State’s D-1641 June water quality standard is: the monthly average of the average outflow for each day must meet or exceed 7000 cfs (monthly average of daily averages). DWR and Reclamation comply with this standard using their own estimation method, not real-time outflow. Figures 2 and 3 below show the differences in the DWR and USGS methods in May-June 2020.

In May-June 2020, DWR and Reclamation maintained Delta outflow (using their own estimation method) near 7000 cfs, except during a mid-May storm when estimated outflow reached a peak of 15,300 cfs (Figure 2). But viewed from a different perspective, there were significant dips in the USGS estimation of outflow during spring tides around June 5 and June 19. The DWR method of estimating didn’t pick up these dips at all. These periods where USGS showed negative net outflow showed up in the monitoring of salinity as well (Figures 4-6). Periods of low or negative outflow were also periods of high salinity at key Delta monitoring stations.

Although net daily Delta flows are relatively small compared to real-time tidal flows (Figures 7 and 8), net flows affect water quality and fish habitat conditions on a daily basis. The salinity data for May-June 2020 at False River (Figure 5) is particularly significant. (Note the spikes in salinity during spring tides around June 5 and June 19). False River is the gateway to Franks Tract. As salinity increases in False River, smelt will move upstream (towards lower salinity conditions) in Franks Tract. As I described in an April 28, 2020 post, Franks Tract is a “smelt trap” where smelt that enter almost invariably perish.

Increasing the standard for June Delta outflow so that the required monthly average of the average outflow for each day is 10,000 cfs, not 7,000 cfs, would not fully offset the effects of spring tides and the use of averaging in DWR’s method of calculating compliance. But it would help protect Delta habitat from salt intrusions during spring tides and keep the low salinity zone and young Delta smelt out of the Delta. Although DWR and Reclamation did a good job in May-June 2020 of staying above 7000 cfs each day using their calculated outflow method, adding an explicit minimum daily flow standard to the monthly flow standard could also help. This would likely have the result of reducing exports during periods of the spring tides in the monthly lunar tidal cycle.

Figure 1: Daily outflow estimated by DWR and USGS in summer 2018.

Figure 2. DWR’s calculated Delta outflow in May-June 2020. Note switch to July standard of 5000 cfs

Figure 2. DWR’s calculated Delta outflow in May-June 2020. Note switch to July standard of 5000 cfs outflow on July 1. Source: CDEC.

Figure 3. USGS’s estimate of tidally filtered Delta outflow as estimated in May-June 2020. Spring-tides occurred May 9, May 23 (not measured because of storm inflows), and also on June 5 and June 19. Note dips in outflow on June 5 and 19; these dips do not appear in DWR’s estimate in Figure 2.

Figure 4. Salinity (conductivity) in eastern Suisun Bay at Collinsville in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 5. Salinity (conductivity) in False River in west Delta in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 6. Salinity (conductivity) in eastern Suisun Bay at Pittsburg in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 7. Hourly river flow and tidally filtered flow in lower San Joaquin River channel in western Delta at Jersey Point in June 2020. Note highly negative peak flows with spring tides on June 5 and June 19.

Figure 8. Hourly river flow and tidally filtered flow in lower Sacramento River channel in western Delta at Rio Vista in June 2020. Note spring tides on June 5 and June 19.

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.