Shasta River Update – April 2019

A February 20, 2019 article in the Eureka Times-Standard reported continuing improvement of Klamath River fall-run Chinook.

“The number of natural area spawners was 53,624 adults, which exceeded the preseason expectation of 40,700. However, the stock is still in “overfished” status as escapement was not met the previous three seasons. The estimated hatchery return was 18,564 adults for the basin.

Spawning escapement to the upper Klamath River tributaries (Salmon, Scott, and Shasta Rivers), where spawning was only minimally affected by hatchery strays, totaled 21,109 adults. The Shasta River has historically been the most important Chinook salmon spawning stream in the upper Klamath River, supporting a spawning escapement of 27,600 adults as recently as 2012 and 63,700 in 1935. The escapement in 2018 to the Shasta River was 18,673 adults. Escapement to the Salmon and Scott Rivers was 1,228 and 1,208 adults, respectively.”

In a May 2017 post, I discussed an increasing contribution to the Klamath run from the Shasta River.  In Figure 1 below, I have updated my original spawner-recruit analysis from the prior post with 2017 and 2018 escapement numbers for the Shasta River.  The Shasta run in fall 2018 was third highest on record for the Shasta River.  The river’s fall-run population continues to benefit from improved water management.  Coho salmon and steelhead have yet to show significant improvements (Figure 2).

An February 26, 2019 article from the publication Grist (posted in 2/26/19 Maven’s Digest) describes changes to water management in the Shasta River.  The Nature Conservancy, using public grant funds, purchased the nearly 5000-acre Shasta Big Springs Ranch for $14 million in 2009.  More recently, the California Department of Fish and Wildlife purchased the water rights of the Shasta Big Springs Ranch.  Now, more water is left in the Shasta River, and only a third (1500 acres) of the ranch remains irrigated.  The article in Grist states that the new allocation of water has negatively affected the ranch’s ability to support wildlife and threatened its ability to support ranching.  In addition, the article questions the benefits of the new management regime to fish: “[T]he fish don’t seem to be doing much better either.”

While some will argue the relative values of ranching and fish protection,  I see no grounds to argue that changes in water management have not been positive to the Shasta River and Klamath River salmon.  Summer flows in the river below the ranch appear to have improved over the long term average (Figure 3).  Many of the Shasta River’s Chinook and Coho salmon spawn in the Big Springs area and in the river below Big Springs, and depend on flow and cold water input from the springs.  Even with the contribution of this flow, water temperatures are marginal (>65oF) for young salmon from May to September (Figure 4).

From my perspective, the loss of several thousand acres of irrigated pasture out of roughly 25,000 acres in the Shasta Valley seems a small price to pay for a large step towards the recovery of Shasta and Klamath River salmon.

Figure 1. Spawner-recruit relationship for Shasta River. Escapement estimates (log10X – 2 transformed) are plotted for recruits by escapement (spawners) three years earlier. Year shown is recruit (escapement) year. The number is the year that fish returned to the Shasta River to spawn. The color of the number depicts the water-year type in the Shasta River during the year the recruits reared. The color of the circle depicts the water-year type in the Klamath River during the year the recruits reared. Blue is for Wet water-year types. Green is for Normal water-year types. Red is for Dry water-year types. Example: 90 depicts fish that returned to the Shasta River as adult spawners in 1990. These fish were spawned in 1987 and reared in winter-spring 1988. The red number shows that the 1988 rearing year was a Dry water year in the Shasta River; the red circle shows that the 1988 rearing year was a Dry water year in the Klamath River. Note very poor recruits per spawner in 1990-1993 drought period, compared with relatively high recruits per spawner from 2011-2018, even though the latter period included the 2012-2016 drought.

Figure 2. Shasta River salmonid runs from 1930 to 2017. Source: https://www.casalmon.org/salmon-snapshots/history/shasta-river

Figure 3. Shasta River flows in the Shasta River below Big Springs 2016-2018 with 30 year average. Note summer base flow appears to have improved by approximately 10-30 cfs.

Figure 4. Water temperature in the Shasta River below Big Springs including summers of 2017 and 2018. Source: DWR CDEC.

 

 

No Funding Help for Central Valley Salmon Hatcheries: Sacramento Valley Salmon Recovery Program and Proposition 3 Strike Out

California’s salmon hatchery programs badly need major projects and upgrades.  The future of wild and hatchery salmon runs, as well as commercial and sport fisheries in California, depends on these programs.  However, hatchery programs are operated and funded under antiquated water project mitigation programs that lack a progressive approach (and funding) for hatcheries in salmon ecosystems in California.  And neither the Sacramento Valley Salmon Recovery Program (SVSRP) nor Proposition 3 includes investments in hatcheries.

California Salmon Hatcheries:

  • Iron Gate Hatchery: Coho, Fall Chinook and Steelhead (Klamath River)
  • Trinity River Hatchery: Coho, Fall Chinook, Spring Chinook and Steelhead (Trinity River)
  • Nimbus Hatchery: Fall Chinook and Steelhead (American River)
  • Mokelumne Hatchery: Fall Chinook and Steelhead (Mokelumne River)
  • Merced Hatchery: Fall Chinook (Merced River)
  • Feather River Hatchery: Fall Chinook, Spring Chinook and Steelhead (Feather River)
  • Coleman National Fish Hatchery: Fall Chinook, Late-fall Chinook and Steelhead (Battle Creek)
  • Livingston Stone National Fish Hatchery: Winter Chinook (Sacramento River)

The California Hatchery Review Project and Hatchery Science Review Group (HSRG)1 identified major problems/issues, goals, and expectations related to California salmon hatcheries:

  • Serious loss and degradation of habitat limits natural production of salmon and steelhead in California.
  • Hatchery program goals have been consistently expressed in terms of juvenile production rather than adult production.
  • Program purposes have not been clearly defined.
  • Hatchery monitoring and evaluation programs and Hatchery Coordination Teams are needed.
  • Program size has been set independent of any consideration of potential impacts of hatchery fish on affected natural populations.
  • Off-site releases promote unacceptable levels of straying among populations.
  • Marking/tagging programs are needed for real-time identification of all hatchery-origin Chinook salmon returning to hatchery facilities.
  • Standards for fish culture, fish health management and associated reporting are inadequate and need to be improved.
  • Populations and population boundaries have not been established for non-listed species and are needed for effective development of integrated hatchery programs.
  • Harvest management of Sacramento River Fall Chinook should account for the productivity of naturally-spawning adults.

Program goals:

  • Improving the efficiency of hatchery operations
  • Reducing the impact of hatcheries on natural populations
  • Supporting commercial, tribal, and recreational fisheries

Expectations from hatchery programs:

  • Reduction in the domestication of hatchery fish
  • Reduction in the negative impacts of hatchery fish on natural spawning populations
  • Improved prospects for the long-term successful coexistence of hatchery and natural fish

NMFS’s Salmon Recovery Plan, in addition to supporting the recommendations of the HSRG, also promotes the following action:  “Develop and implement an ecosystem based management approach that integrates harvest, hatchery, habitat, and water management, in consideration of ocean conditions and climate change (Lindley et al. 2009).”

Because scientific studies have shown that hatcheries reduce the long-term fitness and survival of salmon species, and California’s listed salmon and steelhead cannot be sustained without hatcheries, it is imperative that hatchery programs be upgraded to safeguard the future of salmon in California.  One way to accomplish this goal and the others described above is to adopt the goals and objectives of a Conservation Hatchery Strategy.

First, there needs to be a shift away from hatcheries as mitigation for long-ago-built dams and water diversions, and a shift toward hatcheries contributing directly to salmon recovery and conservation.  Dumping tens of million salmon and steelhead hatchery smolts at the eight hatcheries or trucking some to the Bay may sustain a minimal coastal fishery, but it will not bring recovery or delisting of endangered populations.  Conservation hatcheries are a necessary tool for salmon recovery.

The eight hatchery programs need funding to convert them to conservation hatcheries.  That funding could come from the SVSRP and resource agency programs, and future ballot initiatives, as well as mitigation programs.  At a minimum, the SVSRP should be integrated into an ecosystem-based management approach that includes conservation hatcheries.

Sacramento Valley Salmon Resiliency Strategy

The Sacramento Valley Salmon Resiliency Strategy, June 2017, is the state’s strategy to improve the resilience of listed salmon to its activities, including water rights permits, State Water Project actions, CESA implementation, and CDFW management.

The document states on page 2:

Specific biological objectives have been identified for the Sacramento River that support the general need to increase survival and productivity of salmonids in the Sacramento Valley and to increase life history and genetic diversity. A summary of these biological objectives:

  1. Increase productivity by improving spawning and incubation conditions (habitat and water quality).
  2. Increase productivity by increasing juvenile salmonid survival.
  3. Support the full range of juvenile migration conditions to maintain life history diversity.
  4. Support the full range of adult migration conditions to maintain life history diversity.
  5. Maintain genetic integrity by limiting genetic influence from hatchery-produced fish and interbreeding of genetically or behaviorally distinct runs.

The Strategy is an aggressive approach to improving species viability and resiliency by implementing specific habitat restoration actions. (Emphasis and bullet numbering added)

The Strategy is defined as a “resiliency” strategy and not a recovery strategy for a reason. It does not include the actions necessary for recovery. It won’t fix the activities that caused the crisis in the first place. Over the past several decades, much restoration has occurred, yet fish populations continue to decline. Much stronger and more immediate management actions are needed to save the salmon populations. Habitat restoration alone will simply not suffice.

So what is missing?

  1. Spawning and incubation conditions – Missing are actions to maintain cold water temperatures and sufficient spawning flows in the reaches below all the major dams during spawning and incubation. A. Eliminate the water temperature increases caused when water from Whiskeytown Reservoir is routed through Spring Creek Powerhouse to Keswick Reservoir. B. Maintain cold water in the Sacramento River downstream to Red Bluff, not just to Redding. C. Eliminate dewatering of winter, spring, and fall–run salmon redds in the Sacramento River. D. For the American and Feather rivers, take actions similar to A through C that maintain cold water and eliminate redd stranding. E. Better manage reservoirs to place more emphasis on cold water pools and less on water deliveries.
  2. Juvenile salmon survival – Maintain adequate flows and water temperatures in rearing reaches to sustain growth and to reduce stress and predation.
  3. Full range of juvenile migration conditions – Maintain adequate flows and water temperatures in the lower rivers and the Delta throughout emigration seasons. Do not shave off early and late seasons.
  4. Adult migrations – Maintain adequate flows and water temperatures to assure adult survival, egg survival and gonad development during migration. Do not shave off early and late seasons.
  5. Genetic integrity – Move more toward conservation hatchery activities, reduce straying by barging smolts, implement natural floodplain rearing, mark all hatchery smolts, and introduce mark-selective recreational fisheries.

As for other planned actions like completing projects on Battle Creek and reintroducing salmon upstream of Central Valley rim reservoirs, let’s get on with it. If we keep the present snail’s pace, there is little hope for future salmon generations.

Sites Reservoir —
Potential Benefits for Fish,
Potential to Worsen Conditions for Fish
Working Presumption: Thumbs Down

The proposed Sites Reservoir1 would be a new off-stream storage reservoir covering 12,000 -14,000 surface acres with 1.8 million acre-ft of storage capacity on the west side of the Sacramento Valley (Figure 1). The project would capture and store unregulated Sacramento River winter-spring runoff and some water previously stored in Shasta Reservoir. The diversion capacity to the reservoir would be 5400-6500 cfs, supplied by two existing river diversions (up to 1800 cfs at Red Bluff; up to 2100 cfs at Hamilton City) and a new diversion near Colusa (proponents are evaluating alternative capacities of 1500 and 3000 cfs, in addition to the currently preferred capacity of 2000 cfs). The Sites Authority webpage estimates that it could have diverted over 1 Million acre-ft to storage in Sites in 2018 and 1.8 Million acre-ft to storage in 2017; these figures assume bypass flow requirements at the diversion points and at Freeport, and sufficient storage capacity in the reservoir. The Draft Environmental Impact Report/Environmental Impact Statement (DEIR/DEIS) for the Sites Reservoir Project estimates the average annual diversion to Sites storage at about 500,000 acre-ft; actual diversions would vary depending on hydrology and regulatory constraints.

As an off-stream storage reservoir, Sites would store water behind a dam that is not on a major waterway. Water diverted to the reservoir would be pumped into canals from the Sacramento River, and then pumped into the storage reservoir from small holding reservoirs on the canals. The two existing diversions that would fill Sites have modern fish screening facilities. As currently envisioned, a pump-back hydroelectric operation would allow partial recovery of pumping costs.

The Sites project has potential benefits for fish, but also the potential to worsen conditions for fish.

Potential Benefits for Fish

  1. Under current operations, existing irrigation diversions on the Sacramento River draw water primarily in spring and summer via several major canal systems on the west side of the Sacramento Valley. These diversions draw mainly on water that was previously stored in Shasta Reservoir and released to the Sacramento River in part to keep river water temperatures cool. Shasta Reservoir’s cold-water pool varies in volume depending on storage and other factors, and can run out if it is not managed carefully. If the cold-water pool is depleted at the end of the summer, this threatens the viability of winter-run salmon. Under current operations, spring and summer irrigation diversions from the Sacramento River also cut flow and raise water temperatures in the lower river, which harms salmon, steelhead and sturgeon. Water diverted to storage in Sites in the winter could substitute for some of the spring and summer irrigation deliveries that currently come from Shasta. A greater percentage of water released from Shasta in spring and summer could then flow all the way to the Delta. More water could also be retained in Shasta Reservoir to protect the Shasta cold-water pool into the fall and as carryover for the following year.
  2. If more water were delivered to the Delta from Shasta Reservoir in the spring and summer, less water would theoretically be needed from Folsom and Oroville reservoirs to meet Delta water quality, outflow and other requirements. This could allow more targeted releases of water into the lower American and lower Feather rivers to protect fish in those waters. It could also allow better maintenance of cold-water pools and greater carryover storage in Folsom and Oroville, also very important for the respective fisheries downstream.
  3. Water stored in Sites could be delivered directly to the Delta via the Colusa Basin Drain (CBD) system and Yolo Bypass, reducing outflow demands from other Valley reservoirs. Water delivered directly to the Delta from Sites would be of higher potential productivity and could stimulate winter-spring Bay-Delta plankton blooms that would benefit Delta native fishes.

Potential to Worsen Conditions for Fish

  1. The proposal includes a new point of diversion on the Sacramento River with a capacity to divert 2000 cfs. This would give the project higher diversion capacity and the capability of diverting tributary runoff that would otherwise be unavailable to the two upper river diversions that now enters the Delta. This diversion would also affect flows and water temperatures in the lower Sacramento River, and subject migrating juvenile salmon, sturgeon, and steelhead to a third large screening facility. The new point of diversion would be particularly problematic if it diverted water outside the peak runoff season (late fall through spring).
  2. The new diversion and the reoperation of canal intakes at Red Bluff and Hamilton City to divert water in winter would compete for water with Delta diversions and would affect Delta outflow to the Bay.
  3. Water deliveries and hydropower releases from Sites Reservoir to the lower river at the new diversion site could affect water quality in the lower Sacramento River.
  4. With available winter off-stream storage, the existing diversions at Red Bluff and Hamilton City would be capable of diverting uncontrolled flows from tributaries that have otherwise remained relatively untouched down to the Delta.
  5. The greater diversion capacity may increase demands on Shasta storage and will increase diversion of uncontrolled tributary flows, further compromising fishes in the Sacramento River and the Bay-Delta.
  6. A small but potentially significant amount of water supply stored in Sites Reservoir would be lost to evaporation and groundwater seepage.

Above all, there is too much unknown to evaluate how Sites would affect fish.

As is the case for most proposed water supply projects, the project description in the draft DEIR/DEIS for Sites describes several potential configurations of project infrastructure and a description of proposed constraints. The DEIR/DEIS does not evaluate different constraints, such as different bypass flow requirements past each point of diversion; the DEIR/DEIS only evaluates one value for each point. In spite of numerous requests that the DEIR/DEIS evaluate project diversions with more stringent Delta flow and water quality requirements than the existing inadequate ones, the DEIR/DEIS only evaluates project yield with existing Delta constraints.

The benefit side is even more vague and conceptual. The entire construct of hypothetical Sites benefits would in fact require a new type of proscriptive rules and enforcement mechanisms that would be unprecedented for California water projects. There is simply no clue in any of the Sites literature what those rules would be or even could be.

The project description places no numbers on how much water stored in Sites the project’s operators would dedicate to actions designed to benefit fish. The project description defines no decision-making process for dedicating water to fish, other than to say that on an overarching basis fish agencies will decide. The project description defines no way in which project operators will apportion water for fish against water for water supply. For all the offsets that seem to comprise the lion’s share of fish benefits, the project description does not say how water from Sites will generate improvements in operation of state or federal reservoirs, or whether it will be Sites operators or state and federal operators who make the calls.

Then there is the question of whether there would be any offsets at all. There is no assurance that there will be any decreases at all in water use from Shasta or from other state and federal reservoirs. Water freed up by using Sites to meet Sacramento Valley water supply could simply allow Sac Valley water users to irrigate more land or sell more water for export at the Delta pumps. The DEIR/DEIS proposes no mechanism of enforcing offsets: who would regulate the project’s use of water, who would manage the interaction between Sites water and water from Shasta, Oroville, Folsom and perhaps Trinity reservoirs, and how and against whom any requirements would be enforced.

There are other problems. A shift to winter-spring diversions and use of canal systems would potentially change groundwater recharge and use patterns in the Sacramento Valley. The project would compete for water available to the proposed WaterFix Twin Tunnels project in the Delta. Sites and WaterFix have their “sights” on the heretofore untouched tributary inflows that are also protected by Delta export OMR limits so the flows reach the Bay. There will be a big fight over this uncontrolled water that now makes up a significant portion of the Bay’s freshwater input in drier years. Both projects have claimed future benefits of the same pot of water.

Conclusion

There are potential benefits from Sites project’s main features to Central Valley fishes, including salmon, steelhead, sturgeon, smelt, and striped bass. Most of the benefits would result from switching the diversion time period of the two existing upper river diversions and Shasta reservoir releases to these diversions. The added new diversion and increase in winter diversions will at important times reduce Sacramento River flow and Bay-Delta inflow and outflow, harming fish in certain but sometimes hard to quantify amounts.

Past water developments in the Central Valley have overwhelmingly made conditions for fish worse. The Sites project proponents claim that their project will be different. These proponents have not done themselves, the public, or public policy any favors by relying on generalities and politics as the centerpieces of their efforts to advance their project. At this time, there are too many unknowns to meaningfully evaluate the possibility that benefits might outweigh the harm and justify the costs. In the meantime, it is a reasonable working presumption that the Sites project will worsen conditions for fish as well.

Figure 1. Proposed Sites Reservoir and associated infrastructure on west side of the Sacramento Valley.

Sacramento River Salmon and Water Right Order 90-5

Operation of the Central Valley Project’s Shasta-Trinity Division is governed in part by the State Water Board’s Water Right Order (WRO) 90-5. Issued in 1990, this Order prescribes reasonable protection for Sacramento River salmon, steelhead, and sturgeon even under today’s conditions. The problem in recent years is that “requirements” are not being met by the Bureau of Reclamation.

Even in the past three non-drought years, including record wet 2017 and this year’s normal classification, Reclamation has not met requirements. This has caused significant impacts to salmon, steelhead, and sturgeon, which I have documented in prior posts. In the past three years, Reclamation has used its poor performance during the 2013-2015 drought and global warming as excuses to prioritize preserving water storage in Lake Shasta over meeting water temperature requirements for the Sacramento River under WRO 90-5. But while Reclamation has argued it must preserve Shasta Reservoir’s cold-water pool, Reclamation has maintained full deliveries to its Sacramento Valley contractors.

The State Board has a whole website dealing with the issue and problems dealing with Reclamation on the issue: (https://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/ ).

In a March 14, 2018 letter to Reclamation, the State Board’s Deputy Director for Water Rights wrote to Reclamation on compliance with WRO 90-5,1 stating:

As you know, Order 90-5 requires Reclamation to maintain a daily average temperature (DAT) of 56 degrees Fahrenheit (F) in the Sacramento River at Red Bluff Diversion Dam during times when higher temperatures will be detrimental to fish, unless factors beyond Reclamation’s reasonable control prevent it from maintaining such temperatures. If Reclamation is unable to meet the temperature requirement at Red Bluff Diversion Dam throughout the temperature control season, Reclamation must develop an operations plan for approval by the Chief of the State Water Board’s Division of Water Rights (Deputy Director). The plan, which is required to be developed in consultation with the California Department of Fish and Wildlife, U.S. Fish and Wildlife Service, National Marine Fisheries Service (NMFS) (collectively fisheries agencies), and the U.S. Western Area Power Administration (WAPA), must designate a location upstream of Red Bluff Diversion Dam where the temperature requirement will be met. Order 90-5 includes specific monitoring and reporting requirements in addition to a general requirement (Condition 3) that Reclamation conduct such monitoring and reporting as is required by the Deputy Director to ensure compliance with the terms and conditions of Order 90-5.

Given potential concerns with temperature management this year and the degraded status of the winter-run Chinook salmon population following the drought, Reclamation should be aware that operational changes may be needed beyond those proposed by Reclamation in their TMP to minimize impacts to winter-run Chinook salmon and avoid redirected impacts to other native species. Reclamation should acknowledge those needs in its TMP and provide for a process for continually evaluating conditions and operations to ensure that needed adjustments to temperature control operations are considered in a timely manner.

On April 2, 2018, Reclamation responded2:

This response not only states that Reclamation will not meet WRO 90-5 water temperature requirements at Red Bluff (river mile 243), but also that it will not meet these requirements at Balls Ferry (river mile 276), 30 miles upstream and half way to Keswick Dam. In fact, Reclamation to date has blatantly kept the promise of not meeting requirements (Figure 1), despite the fact that Shasta Reservoir is full of cold water. It is not even May yet!

The Coleman Fish Hatchery just stocked 4 million fall-run salmon hatchery smolts at Battle Creek upstream of Red Bluff, with another 2 million soon to follow.3 The recently released hatchery fish (and their wild counterparts) are being subjected to highly stressful conditions in their 200-mile journey to San Francisco Bay (Figures 2 and 3).

There is plenty of cold water in Shasta Reservoir (Figures 4 and 5) to meet the flow and temperature needs of salmon in the lower Sacramento River through the summer, as required by WRO 90-5. It would take a total release of about 6000 cfs from Shasta to meet WRO 90-5 requirements at this time just at Balls Ferry. Reclamation increased releases in the past several days to 5300 cfs to meet water contractor demands. The problem remains that this water is not reaching the lower river, where water temperatures now hit 70°F and exceed the WRO 90-5 limits of 68°F (Figure 3). It will take an added 2000-3000 cfs at Wilkins Slough to keep the lower river below its 68°F limit This added release would represent about one foot of Shasta Reservoir water-surface elevation per week (Figure 4).

Sacramento Valley contractors have been given a 100% water allocation. South of Delta San Joaquin CVP contractors have been allocated only 40%. Reclamation is fully capable of meeting WRO 90-5 requirements, as it did historically. It is up to the State Board to enforce the CVP permit requirements. Given the state of the salmon populations, there should be no compromise on the permit requirements.

Figure 1. Reclamation report on Sacramento River temperatures through 24 April, 2018. Source: https://www.usbr.gov/mp/cvo/vungvari/sactemprpt.pdf

Figure 2. Water temperature at Red Bluff (RM 243), April 2018. Red line is limit requirement in WRO 90-5. Source: cdec.

Figure 3. Water temperature at Wilkins Slough (RM 118) April 2018. WRO 90-5 limit is 68°F. Water temperatures in excess of 65°F are highly stressful to juvenile salmon. Source: cdec.

Figure 4. Shasta storage characterization for water at the dam’s temperature control device (TCD), March 23 – April 22, 2018. Source: https://www.usbr.gov/mp/cvo/vungvari/ShastaTCD2018.pdf (See link for updates.)

Figure 5. Shasta Reservoir storage as of April 24, 2018.
Source: http://cdec.water.ca.gov/resapp/ResDetail?resid=SHA

  1. https://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/docs/2018/03142018_sac_temp_plan_ltr.pdf
  2. https://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/docs/2018/04022018response_90_5.pdf
  3. Note that Coleman Fish Hatchery on Battle Creek normally stocks 12 million fall-run smolts, but brood year 2014 salmon did not provide sufficient spawners (eggs for hatchery), and the hatchery thus produced only 6 million smolts in 2017. Hopefully, the 2 million smolts that have not yet been released will be trucked to the Bay.