Saving Wild Salmon in Dry Years

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:—-smolt-project-monitors-kasilof-river/

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

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

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

Salmon Drought Plan – there is no plan

A Salmon Drought Plan (with implementation) is badly needed. For the past two years, what we had instead was delayed reaction, an ad hoc hodge-podge of underfunded bandaid actions that didn’t come close to protecting salmon. The state and federal agencies called this “real-time” response. Huge injury to salmon resources occurred, and the triage center was a dysfunctional “Mash” unit.

Subtitle C of Section 421 of H.R. 2983, Congressman Huffman’s bill1 on drought assistance and improved water supply reliability, provides for preparation of a California Salmon Drought Plan and $3,000,000 for implementation. The measures in the bill would be a reasonable beginning:

(a) SALMON DROUGHT PLAN.—Not later than January 1, 2016, the United States Fish and Wildlife Service shall, in consultation with the National Marine Fisheries Service, the Bureau of Reclamation, the Army Corps of Engineers, and the California Department of Fish and Wildlife, prepare a California salmon drought plan. The plan shall investigate options to protect salmon populations originating in the State of California, contribute to the recovery of populations listed under the Endangered Species Act of 1973 (16 U.S.C. 1531 et seq.), and contribute to the goals of the Central Valley Project Improvement Act (Public Law 102–575). The plan shall focus on actions that can aid salmon populations during the driest years. Strategies investigated shall include—
(1) relocating the release location and timing of hatchery fish to avoid predation and temperature impacts;
(2) barging of hatchery release fish to improve survival and reduce straying;
(3) coordinating with water users, the Bureau of Reclamation, and the California Department of Water Resources regarding voluntary water transfers, to determine if water released upstream to meet the needs of downstream or South-of-Delta water users can be managed in a way that provides additional benefits for salmon;

(4) hatchery management modifications, such as expanding hatchery production of listed fish during the driest years, if appropriate;
(5) increasing rescue operations of upstream migrating fish; and
(6) improving temperature modeling and related forecasted information to predict water management impacts to salmon and salmon habitat with a higher degree of accuracy than current models.

However, Congressman Huffman’s bill, proposed as part of an alternative to still-pending legislation that would make conditions for fish worse, has not moved forward.

Why is it left to a California congressman to try to get a drought salmon program going? The state and federal resource agencies have huge staffs that are more than capable of taking action and immediately preparing a joint plan of action. Government grant programs have funded numerous NGO scientists who could participate. The state has a drought plan for cities and farms. Why isn’t there one that protects the state’s salmon resources? CDFW’s drought planning effort is outdated.2 There is no federal plan. For the past two years, the fisheries agencies have simply concurred with every Temporary Urgency Change Petition to weaken fish protections coming from the California Department of Water Resources and the Bureau of Reclamation, leaving protection of resources to the State Water Board (which also failed to step up).

California needs a salmon drought plan now.

Yuba River Fisheries Enhancement

Improving Yuba River Fisheries

The Yuba River (Figure 1), including the lower river below Englebright Dam and its three upper forks and two reservoirs, provides a substantial fisheries resource. But it could provide much more.

Overall, the Yuba has a long complicated story with a colorful history that goes back to the gold rush and hydraulic mining in the last two centuries. Nearly two decades ago the CALFED program took on the Yuba fisheries as a special case.1 Options in these management planning efforts have included building a hatchery, trucking salmon and steelhead above the dams, removing dams, providing better upstream passage at dams, raising young salmon in rice fields, and enhancing spawning and rearing habitat in the lower river below Englebright Dam. Last year the National Marine Fisheries Service published its Central Valley Recovery Plan for threatened and endangered salmon and steelhead that included actions for the Yuba River.2 As prescribed in the Recovery Plan, The Yuba Salmon Partnership Initiative recently came to an agreement to trap and haul salmon above New Bullards Bar Reservoir to the North Yuba.3 The US Army Corps of Engineers and Yuba County Water Agency have also teamed up to enhance fish habitat and passage, and recently asked for public input.4 Their responsibility stems from the dams, flood control, water supply, and hydroelectric production on the Yuba River.

Yuba River Map

Figure 1. Yuba River is a tributary of the Feather River in the Sacramento Valley north of Sacramento, California. The lower river flows about 25 miles from Englebright Dam to to its mouth on the Feather River. New Bullards Bar reservoir on the North Yuba completed in 1970 is one of the largest in California, with storage of 966,000 acre-feet.

Status of Fisheries

Lower Yuba Trout Fishery

The gem of the Yuba is its lower river “blue-ribbon” wild trout fishery that extends from Englebright Dam downstream to Daguerre Dam and below, a total of about 20 river miles. The trout here are predominantly wild, except for some stray Feather hatchery steelhead smolts that migrate up from the Feather River, and for wild and hatchery trout from upriver that pass downstream from the dams. The wild trout of the lower Yuba have their own distinct character, likely derived from mixed genetics including steelhead. They grow quickly due to year-round near-optimal water temperature and to abundant tailwater insects supplemented with salmon eggs and fry. Trout survive well in the reach between Englebright Dam and Daguerre Dam in part because striped bass and other predatory fish cannot ascend Daguerre’s ladders. They are also protected by strict sport fishing regulations that limit gear, harvest, and season.

Lower Yuba Steelhead Fishery

The lower Yuba steelhead fishery is very limited, made up of small numbers of Feather hatchery strays and a very few wild steelhead. It is much the same case as in the lower Sacramento River near Redding, where wild resident trout dominate the fishery. There is no steelhead stocking on the lower Yuba, although many Feather hatchery steelhead smolts migrate into the lower Yuba and take up residence.

Spring Run Chinook Salmon

The number of spring run Chinook is also small, and is made up mostly of stray Feather River hatchery fish. Small numbers of adult spring run spend the summer milling below Englebright dam waiting to spawn in early fall. The population suffers from the flawed “summer run” genetics of the Feather River hatchery program, lack of spawning habitat below Englebright, and competition and interbreeding with fall run in the lower Yuba.

Fall Run Chinook Salmon

Abundant some years and not in others, the fall run salmon follow the trends of the Feather hatchery fall run, mainly because they are mostly Feather hatchery strays or their offspring. Like other Central Valley fall run, production suffers severely in drier years when winter flows are low and unable to carry newly emerged fry to their nursery areas in the Delta and Bay. Habitat and survival is poor for fry that remain in the rivers because of a lack of backwater and floodplain habitat and woody in-stream cover. The Yuba, like the Sacramento and its other tributaries the Feather and American, and like the San Joaquin and its tributaries, suffers from winter-spring reservoir storage of most of the dry year runoff, leaving little flow to help young salmon emigrate or to provide floodplain rearing habitat.

Recommended Actions

I recommend the following actions to help improve the populations of the target fish species to protect them from extinction, but also to improve the dependent sport and commercial fisheries.

  1. Adult Spring Chinook should be captured at Daguerre Dam and trucked above the dams to spawn. Young thus produced should be captured and transported below Daguerre Dam in wetter years or trucked to Verona (mouth of Feather River) and barged to the Bay in drier years. Spring run should not be allowed to spawn in lower Yuba where they interbreed with fall run or have their redds destroyed by fall run spawners.
  2. Spawning and rearing habitats in the lower Yuba should be enhanced as proposed in the above-described programs. Of greatest need are woody cover in low flow channels and low flow spawning and rearing habitats such as alcoves, side channels, and connected oxbows.
  3. Winter-spring flows in the lower river should be enhanced when necessary to improve emigration of young salmon and steelhead in wet, normal, and below normal water years given sufficient reservoir inflows and storage supplies.
  4. In dry years, wild fall run salmon and steelhead young should be captured in winter and spring at Daguerre Dam and trucked to Verona and then barged to the Bay.
  5. A conservation hatchery should be considered for the lower Yuba to enhance the spring run salmon and steelhead populations. Alternatively, repurposing of a portion of the Feather River Fish Hatchery to achieve this enhancement should be considered The first order of business would be to develop appropriate genetic stocks; the second would be to increase production and contribute to sustainable fisheries.

These and other suggestions are also generally prescribed in the following blog post by Dr. Peter Moyle (UC Davis): .