Category Archives: Restoration

Winter Run Salmon – “Species in the Spotlight”

Posted on by

Winter Run

Species in the Spotlight

The National Marine Fisheries Service (NMFS) has included the Sacramento River Winter-Run Chinook Salmon in its “Species in the Spotlight,”1 one of the eight species under NMFS’s jurisdiction nationwide that are most at risk of extinction.

On its website, NMFS describes the condition of Winter-Run (in italics below):

State and Federal Agencies, public organizations, non-profit groups and others in California’s Central Valley have formed strong partnerships to save Sacramento River winter-run Chinook salmon. Efforts to protect winter-run Chinook salmon include restoring habitat, utilizing conservation hatchery programs, closely monitoring the population, and carefully managing scarce cold water. Additional key actions needed to safe guard winter-run Chinook salmon from further declines include:

  • Improving management of Shasta Reservoir’s storage in order to provide cold water for spawning adults, eggs, and fry, stable summer flows to avoid de-watering redds, and winter/spring pulse flows to improve smolt survival through the Delta. (Note: badly needed as these actions have been generally lacking especially in the past two years.)
  • Completing the Battle Creek Salmon and Steelhead Restoration Project and reintroducing winter-run Chinook salmon to the restored habitat. (Note: Badly needed with little progress made in regard to Winter Run.)
  • Reintroducing winter-run Chinook salmon into the McCloud River. (Note: Badly needed with little progress made.)
  • Improving Yolo Bypass fish habitat and passage so juveniles can more frequently utilize the bypass for rearing and adults can freely pass from the bypass back to the Sacramento River. (Note: Badly needed with little progress made.)
  • Managing winter and early spring Delta conditions for improved juvenile survival. (Note: During the past four years of drought, Delta outflow has almost always been inadequate for emigrating juveniles.)
  • Conducting landscape-scale restoration throughout the Delta to improve the ecosystem’s health and support native species. (Note: Little progress has been made.)
  • Expanding LSNFH facilities to support both the captive broodstock and conservation hatchery programs; (Note: In progress. The hatchery program released 600,000 smolts in February last year and 400,000 in February this year. The releases are made in Redding where flows have been too low for good survival because Shasta Reservoir is retaining all its inflow. Much greater survival would be achieved if the smolts were trucked downstream to mid-river and then barged to the Bay.)
  • Evaluating alternative control rules used to limit incidental take of winter-run Chinook salmon in ocean fisheries. (Note: Ongoing and in progress. Fishery harvest for all races of Chinook will likely be curtailed this year.)

Number One Threat

The most serious threat to Winter Run and the major cause of the nearly complete loss of the past two years’ production relates to the first item in the above list: improving management of Shasta Reservoir cold water storage is essential. The change from a 58°F daily-average water temperature standard at Redding (last summer) to 53°F as proposed by NMFS will greatly help by alleviating sporadic lethal conditions that occurred last summer (Figures 1 and 2).

Achieving non-lethal conditions through the summer is possible by conserving Shasta Reservoir’s cold-water pool, which is best achieved by reducing inputs of warm water from Whiskeytown Reservoir (from Lewiston-Trinity reservoirs) into Keswick Reservoir via the Spring Creek Powerhouse (Figure 3). This source of warm water made up about 15% of the release to the Sacramento River from Keswick Reservoir, and required use of extra Shasta’s cold-water pool water to meet the relaxed temperature standard of 58°F in the upper Sacramento River below Keswick in Redding.

Another source of warm water to Keswick Reservoir was from daily afternoon peak power releases from Shasta Dam (Figure 4). High releases in afternoons raised water temperatures in Keswick Reservoir, requiring more cold-water pool release to compensate for warm water inputs. Apparently, the operations were too complicated for Reclamation to maintain the required 58°F average daily temperature at the mouth of Clear Creek (CCR gage: Figure 1). Operations at other times (e.g., first week in August) indicate clearly that Reclamation had the capability of keeping the water temperature well below lethal levels.

Figure 1. Lethal water temperature extremes for salmon eggs and fry (red circles) near Redding in summer 2015. Green circles denote non-lethal conditions that can be maintained with proper management of Shasta’s cold-water pool.

Figure 1. Lethal water temperature extremes for salmon eggs and fry (red circles) near Redding in summer 2015. Green circles denote non-lethal conditions that can be maintained with proper management of Shasta’s cold-water pool.

Figure 2. Episodes of high water temperature in Keswick Reservoir (red circles) in summer 2015. Peaks were due to hydropower peaking and specific operations of the Shasta Temperature Control Intake Tower to powerhouses at Shasta Dam.

Figure 2. Episodes of high water temperature in Keswick Reservoir (red circles) in summer 2015. Peaks were due to hydropower peaking and specific operations of the Shasta Temperature Control Intake Tower to powerhouses at Shasta Dam.

Figure 3. Warm water (red circle) entering Keswick Reservoir from Whiskeytown Reservoir via Spring Creek Powerhouse in summer 2015. Daily range of 1°F is due to hydropeaking operations.

Figure 3. Warm water (red circle) entering Keswick Reservoir from Whiskeytown Reservoir via Spring Creek Powerhouse in summer 2015. Daily range of 1°F is due to hydropeaking operations.

Figure 4. Warm water releases (red circle) from Shasta Reservoir during daily hydropeaking operations in summer 2015. Release water temperatures in the first week of August and September were lower because of lower afternoon hydropower peaking releases of warm water along with more night-morning cold water pool releases.

Figure 4. Warm water releases (red circle) from Shasta Reservoir during daily hydropeaking operations in summer 2015. Release water temperatures in the first week of August and September were lower because of lower afternoon hydropower peaking releases of warm water along with more night-morning cold water pool releases.

 

Largemouth Bass Production in the Delta

Posted on by

I had the unique opportunity to study fish use of shallow inshore waters of the western Delta in 1978-79 and again in 2004-05. One of the biggest differences I noticed after 25 years was the increase in Largemouth Bass production. Mitigation areas where levees were breached allowing tides to enter-and-leave tidal ponds without flow-through were virtual Largemouth breeding factories. Areas where channel entrances had filled in and circulation reduced also were prone to aquatic plant proliferation and an abundance of non-native lake/pond fish including Largemouth, sunfish, and shiner minnows. Flow-through areas and tidal channels with two ends had lower Largemouth production (and more native fishes). Limited tidal circulation also caused prolific amounts of aquatic vegetation including water hyacinth, Egeria, milfoil, Parrots Feather, and Potamogeton. Dense beds of aquatic vegetation also occurred in bays, dead-end sloughs, breached islands, and protected shorelines.

A recent study1 relates higher Largemouth production to increases in aquatic plants, specifically relating the abundance of young Largemouth to Egeria. They also found young Largemouth more abundant in warmer waters, another feature of backwater areas. Aquatic plants slow currents, capture sediment, and absorb sunlight, which all contribute to warming of shallow waters.

One of the paper’s conclusions related to future habitat restoration:

“While these efforts will expand the largely missing shallow-water habitat in the Delta, a major concern is that increased shallow water area will expand the habitat for Brazilian waterweed and consequently increase the abundance of Largemouth Bass, creating a predation sink for target native fishes (Brown 2003).”

I have some points of disagreement with these conclusions. First, I do not believe the Delta lacks shallow water habitat. The problem, rather, is that too much of existing shallow water habitat is bad habitat more conducive to non-native warm water fish. Second, good shallow habitat along the edges of the bays and rivers has been and continues being lost to riprapping, ship-channel dredging, remnant soft-levee erosion, and filling with sediment.

I concur with the paper that much planned restoration will create more bad habitat. Instead we should be protecting good habitat and converting more of the bad habitat to good habitat.

For more on the subject of Delta habitat restoration see: http://calsport.org/news/cspas-assessment-of-historical-habitat-restoration-in-the-delta/ .

Saving Wild Salmon in Dry Years

Posted on by

I support a radical measure for saving wild salmon production in dry years in some Central Valley rivers under special circumstances: capturing wild juvenile salmon in rivers and transporting them to the Bay. This strategy has been employed in dry years on the Columbia River system, and by East Bay Municipal Utility District (EBMUD) in the present drought on the lower Mokelumne River. Under existing conditions in dry years, over 80% of Central Valley salmon fry, parr, and smolts are lost between spawning grounds and their San Francisco Bay target summer nursery. Without natural winter and spring pulse flows, few young wild salmon are able to navigate and survive to the Bay. Much of the production is lost in winter at the fry stage, which is the natural stage for Central Valley spring-run and fall-run Chinook to migrate to the Bay. Less but still important production is lost during the spring fingerling, pre-smolt, and smolt migration stages. In contrast, the hatcheries bypass the many river and Delta sources of mortality by rearing fry in raceways and trucking smolts to the Bay. It’s no wonder 90% of the salmon along the coast are from hatcheries.

Both practices (transport of hatchery and wild juveniles) should only be used in drier years, when there are minimal winter-spring river flows to naturally transport salmon. However, in drought years when reservoir inflows are low, transporting young salmon to the Bay may be necessary. Millions of wild, naturally-produced fry, parr, and smolts could be saved in each of the Central Valley spawning rivers. Huge numbers of young wild salmon are produced even in drought years in rivers such as the Yuba, American, Mokelumne, and Stanislaus that might otherwise be wasted when the Sacramento and San Joaquin rivers trickle into and through the Delta.

The process of trapping and hauling young salmon was perfected on the Columbia River in recent decades1. Capture of young salmon in the rivers at dams and water diversions is feasible and cost-effective. Many wild salmon fry can be captured at large fish screened diversions with fish bypasses (e.g., Daguerre Dam on Yuba River; GCID diversion on Sacramento River). Young salmon can also be captured in rivers below spawning reaches. For example, on the American River at Watt Avenue and the Yuba River at Hallwood Avenue, there are ideal locations with existing screw traps for indexing young salmon production that could be expanded to capture most of the production in low-flow conditions.

I have seen such bank-to-bank capture systems in Alaska on large very popular fishing rivers. The traps and supporting infrastructure are readily available. Peak trap catch of wild salmon is February-March, when hatchery transport trucks are largely unused, waiting for April-May hatchery transport season ().

Barging from the lower rivers to the Bay in lieu of trucking would help minimize subsequent straying of adults. Sacramento Valley salmon can be “barged” from Knights Landing; Feather-Yuba River salmon from Verona; and American River salmon from Discovery Park.

For more on trap capture systems including the Alaska examples see the following sources:
http://www.sf.adfg.state.ak.us/FedAidPDFs/FRED.011.pdf
http://www.adfg.alaska.gov/static/home/library/PDFs/afrb/toddv1n2.pdf
https://redoubtreporter.wordpress.com/2010/06/30/one-fish-two-fish-red-fish-new-fish-—-smolt-project-monitors-kasilof-river/
http://www.stateofthesalmon.org/fieldprotocols/downloads/SFPH_p8.pdf

trap capture system

  1. Many of the mainstem dams on the Columbia have been retrofitted with smolt capture systems. Captured fish are passed safely downstream around turbines or barged-trucked to the estuary. ↩

Trap and Haul and Reservoir Populations of Chinook Salmon

Posted on by

In a recent paper, Martin Perales, Jay Rowan, and Dr. Peter Moyle call attention to existing naturally breeding populations of Chinook salmon in Central Valley reservoirs.1 Though the California Department of Fish and Wildlife no longer stocks salmon in reservoirs that are capable of reproducing, residual salmon are now surviving in some reservoirs and spawning upstream, and these authors are concerned that these fish could interbreed with salmon that were transported from downstream of these reservoirs. The abstract for their paper opines: “the possibility of behavioral and genetic interactions may lead to complications of restoration efforts via trap and haul programs. The full extent of this phenomenon needs to be documented before trap and haul programs are initiated to reintroduce salmon above reservoirs.”

There are two major efforts substantially underway to trap and haul salmon past major Central Valley rim dams: the Yuba Salmon Partnership Initiative’s plan to move salmon upstream of New Bullards Bar Reservoir on the North Yuba River, and the Bureau of Reclamation’s effort to move salmon upstream of Shasta Reservoir. Both of these programs will take ten years or more to be fully implemented, if indeed they are implemented at all.

There are no Chinook in New Bullards Bar Reservoir.

There is a substantial population of fall-run Chinook in Shasta Reservoir, many of which migrate up the Upper Sacramento River to spawn. Elsewhere, CSPA has advocated that the Bureau consider the McCloud River upstream of McCloud Reservoir as a potential target location for winter-run Chinook. The concern expressed by Perales, Rowan and Dr. Moyle is one reason why that potential location might be worth a second look: the upper McCloud is not accessible to fish that swim upstream from Shasta Reservoir.

The authors also point out that study of these “adfluvial” populations of Chinook may provide insight into the possible behavior and potential success of trapping and hauling Chinook from downstream of the reservoirs. There is some opportunity for this: in ongoing FERC licensing processes, CSPA proposed studying the spawning of Chinook (as well as trout) in the Tuolumne River that move upstream from Don Pedro Reservoir.

But let’s also not get carried away with the concern, or the potential value of existing reservoir populations of Chinook. The “complications” of interbreeding with residual reservoir salmon are among dozens of potential issues and problems that must be addressed and resolved for a program to move winter-run Chinook above Shasta Reservoir to succeed. And the numbers of Chinook salmon moving upstream from Central Valley reservoirs are generally small.

Any reintroduction of salmon upstream of rim dams will require ongoing improvement and adaptation. Any good program will set up management to solve problems, based in substantial part on monitoring of what fish in the river actually do. We should prepare for and embrace the uncertainty and the challenges. We won’t know how reintroduced salmon will behave, and we won’t even know let alone solve all the problems before we start.

If we stop to study “the full extent” of every issue before we move forward, no reintroduction programs upstream of rim dams are likely to happen at all, ever.

Genetics Matters

Posted on by
Showing the catch

Recent catch of Pilot Peak Lahontan Cutthroat at Pyramid Lake.

In a recent post I brought up the subject of using the right breed of Spring Run Chinook for restoring San Joaquin salmon.1 Breeding (genetics) is important when introducing hatchery fish to a natural system. For salmon, the idea is to match the native fish as closely as possible, because the native fish have adapted to the specific river conditions. Researchers have found that salmon in a river system go back to where they were born because of that adaptation. In Alaska, biologists found that salmon were adapted to specific small tributaries on larger rivers, and identified all sorts of locally adapted traits.

Decades ago, the native Lahontan cutthroat in the Pyramid Lake-Truckee River-Lake Tahoe watershed were wiped out and subsequently replaced by another nearby stock. But these fish did not grow to the large size of the native fish. Then, two decades ago the US Fish and Wildlife Service found some of the original native stock that had been transplanted to Colorado. So US Fish and Wildlife brought the native stock back, and the Paiute Hatchery now uses them. They are now naturally reproducing in the Truckee River immediately upstream from Pyramid Lake.2