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

A Foolish Proposal to End the Restoration of San Joaquin River Spring Run Salmon

In a recent editorial,  the Fresno Bee editorial board1 stated that restoring salmon near Fresno in the San Joaquin River below Friant Dam is a “fool’s errand.”  The editorial referred to recent events near Shasta Dam on the Sacramento River:  “This decimation (of Sacramento Winter Run salmon) has occurred despite the best efforts of federal officials to save salmon – and at the expense of irrigation water for farmers. Officials, in fact, sharply curtailed water flows out of Lake Shasta last spring in an attempt to keep sufficient cold water in the system to support the fish.”  The editorial further stated: “If the Sacramento can’t sustain healthy salmon runs without crippling farmers, what are the prospects that the San Joaquin River – with less water and higher temperatures – can flow with spring-run salmon again?  The editorial implies that it is a waste of time trying to save salmon, especially San Joaquin salmon, “at the expense of irrigation water for farmers”.

Well, the Fresno Bee’s editors are wrong.  Both salmon populations can be restored.  The feds’ efforts at Shasta were in fact not their best.  Yes, most of the Winter Run Salmon died in 2015 as in 2014, but the salmon could have been saved (see our recent post).2  Farmers weren’t “crippled” by salmon: there was simply too little water to supply farmers, especially south of the Delta based on water right allocation priorities.  No additional water could have been released from Trinity or Shasta without jeopardizing next year’s water supplies (or salmon).  In both 2014 and 2015, the Sacramento River Settlement Contractors got most of their allocation (75% – over 1 MAF including water from Trinity Reservoir); at the end of 2015 in particular, many transferred water south of Delta.  Again, this was hardly crippling.  The Settlement Contractors could have and should have been allocated less.  They would have survived.  The salmon did not.  The salmon died from mismanagement of the water supplies and hydropower system, and because the managing agencies deliberately allowed water temperatures to stay for months above the safe level for incubating eggs.

There is no reason healthy salmon runs cannot be sustained in both rivers.  Most of the water released for salmon will still go to farmers.

Here is the best strategy for San Joaquin River salmon.

  1. Spring Run Salmon Only – There is a unique opportunity in this program to keep Fall Run and Spring Run apart to allow the native Spring Run to recover. Do not haul Fall Run salmon to the upper river or include Fall Run in the conservation hatchery.
  2. Conservation Hatchery – The San Joaquin needs a conservation hatchery to raise Spring Run salmon of an appropriate genetic stock for the San Joaquin. Such a facility is planned but so far it is only an “interim facility.”3   It is called the Salmon Conservation and Research Facility (SCARF).4  Its plan calls for using Feather hatchery spring run eggs.  That is a problem – the hatchery must start with eggs from native Central Valley stocks (Deer, Mill and Butte creeks), not “summer run” hybrids from the Feather River.  Yes, the San Joaquin is warmer, which is why having Feather “spring run” that migrate in May and June is not a wise choice.  March-April is a better time for adult upstream migrations in the San Joaquin, which is the timing the Deer, Mill and Butte creek stocks can provide.  The program review team recognizes this:  “Moving forward, there is a program goal of reintroducing multiple stocks from more than one spring-running population available, but there are a lot of questions that need to be answered from a genetics standpoint, in order to make sure reproductive success and survivability of progeny is maximized using pedigree-based genetic marking techniques.”5  The draft EIR (p. 6-57) for the new hatchery argues against using eggs from Deer,Mill or Butte creeks as it poses a threat to the  Deer, Mill and Butte creek populations:  “Propagation of fish at the SCARF has the potential to unintentionally change the genetic composition of wild populations and subsequently contribute to reduced survival in natural environments if conservation stock stray into the Sacramento River basin and spawn with wild spring-run stocks. Additionally, conservation stock may stray into other tributaries of the San Joaquin River basin and interbreed with fall-run Chinook, which may interfere with existing wild and hatchery management actions and reduce genetic fitness of these fall-run populations.”6  I contend that using Feather “spring run” that are already “compromised” genetically would pose a greater threat to other Central Valley stocks.  The technical review team seems to recognize this.  The federal Salmon Recovery Plan has a goal of adding more stock diversity to the Central Valley salmon populations to reduce the threat of extinctions.
  3. Trap-and-Haul – The young salmon produced by the conservation hatchery or produced by wild spawning salmon near Fresno should be trapped and hauled to the Bay except in wet years when river flows are high and the lower river is connected. The present plan is to trap the young and transport them for release near the mouth of the Merced River.  Most of these fish would not survive downstream passage through the lower San Joaquin and the Delta except in high flow wet years.  The young fish should be “barged” in boats with live wells and recirculating river water to ensure they continue imprinting on the San Joaquin.  This avoids many problems discussed in the Issue Paper on Delta effects.7
  4. Winter-Spring Pulse Flows in Wet Years – Young Spring Run would migrate downstream to the Bay and Delta from December to February as fry and fingerlings, and March and April as pre-smolts. Adults would migrate upstream in March and April.  In wet years with substantial natural connection, river flows and water supply, supplemental reservoir releases could be made to improve migration survival.  Such conditions may occur after or between storms, or simply to enhance storm flow peaks of less than adequate magnitude.  Such added flows could be coordinated with Sacramento flows and Delta conditions.  Delta conditions (Delta exports, Head of Old River Barrier, and Delta Cross Channel operations) could also be modified to help young San Joaquin salmon in wetter years when they would be passing through the Delta, and in all years when adults pass through the Delta.

As well as being a legal requirement and the correction of a grievous moral injustice, restoration of Spring Run salmon remains a viable goal for the San Joaquin River.

It is time to save the Delta Smelt

Causes of the Decline of the Endangered Delta Smelt

There are multiple threats to the Delta Smelt population that contribute to its viability and risk of extinction. Chief among these threats are reductions in freshwater inflow to the estuary; loss of larval, juvenile and adult fish at the state and federal Delta export facilities and in urban, agricultural and industrial water diversions; direct and indirect impacts of the Delta Smelt’s planktonic food supply and habitat; and lethal and sub-lethal effects of warm water and toxic chemicals in Delta open-water habitats.

Temporary urgency change orders by the State Board have allowed reduced Delta outflow and increased Delta salinity. This has moved the Low Salinity Zone further upstream (eastward) into the Delta, thereby increasing the degree of each of these threats. During the past few drought summers, remnants of the population have been confined to a small area of the Low Salinity Zone where water temperatures barely remain below lethal levels. The change orders are an obvious and direct threat to the remnants living in the Low Salinity Zone. Further allowing these weakened standards to be violated is a direct disregard for the remnants of the population. It places them at extraordinary risk by bringing them further into the zone of water diversions, degrading their habitat into the lethal range of water temperature, further degrading their already depleted food supply, and increasing the concentrations of toxic chemicals being relentlessly discharged into the Delta.

Saving the Delta Smelt

The following are measures necessary to save the remnant Delta Smelt population:

  1. Keep the low salinity zone (LSZ) out of the Delta as prescribed in State water quality control plans over the last several decades. This can be readily accomplished by meeting already defined flow and salinity standards and restrictions on Delta exports. The LSZ on the Sacramento channel side should be in the wide open reach of eastern Suisun Bay between Collinsville and the west end of Sherman Island (location of Emmaton standard). It must be kept out of the Emmaton-to-Rio Vista reach just upstream in the west Delta, because this reach is confined and continually degraded by reservoir releases and warm water passing through the North Delta via Three Mile Slough to the interior of the Delta and south Delta water diversions. On the San Joaquin (south) side, the low salinity zone belongs in the wide Antioch–to-Jersey Point reach as prescribed in standards. This can be accomplished in spring and summer of dry years by maintaining prescribed flows, salinity standards at Jersey Point, installation of the False River and Dutch Slough Barriers, and opening the Delta Cross Channel (which results in positive net outflow from the mouth of Old River downstream to Jersey Point in the Central Delta). Maintaining the net positive flows in west Delta channels helps tremendously in getting salmon, steelhead, sturgeon, striped bass, and smelt from upstream freshwater spawning areas to their downstream rearing area target, the estuary’s LSZ. Keeping the LSZ in eastern Suisun Bay, as has always been an objective Delta Water Quality Plans, has huge indirect benefits as well, including greater plankton production, lower non-stressful water temperatures (conducive to growth and survival of all the Delta fish including smelt and salmonids), higher turbidity levels in the LSZ (reduced predation on and improved feeding for Delta smelt), lower invasive Asian clam concentrations in eastern Suisun Bay (which siphon off plankton and larval fish), and lower concentrations of toxins in the LSZ.
  2.  Improve the physical habitat of the LSZ. Habitat in eastern Suisun Bay, though far better than that of the west Delta, has been continuously degraded over the past century. Fortunately, there are few levees along the north shore of the Sacramento side. However, the wave-swept shores along Antioch Hills have lost all riparian vegetation except pockets of invasive Arundo. Hillside windfarm and shoreline erosion have filled in shoreline shoals, shallows, bays and alcoves that provided rearing habitat for smelt and salmon (salmon fry are the most abundant fish in these shallows through the winter). Miles of shoreline bays, inlets, and tidal marshes east of Collinsville have been lost. On the south side of the Sacramento channel are the remnants of historic Delta marshes and islands of West Sherman Island and Sherman Lake. Gradually the riparian shoreline and shallow waters are washing away as a consequence of wind as well as ship-wake erosion. Lack of interior marsh channel circulation has also led to grand infestations of invasive non-native submergent, emergent, and floating aquatic vegetation. Like the north shore, the south shoreline of West Suisun Bay on the San Joaquin side is not leveed. Likewise, shoreline and shallow water habitats are degraded, but from industrialization. Large areas east of Antioch to Big Break are degraded much as in the area of Sherman Lake. Both the north and south East Suisun Bay channels are degraded by dredging of the two deep-water ship channels, which has resulted in the loss of shallow shoal, bay, and mudflat habitats. Virtually none of the habitats mentioned above were addressed in the grand BDCP restoration plans for the Bay-Delta. Though some of the areas have been prescribed for restoration in various mitigation plans, virtually no progress has been made toward their restoration in the last several decades.
  3. Stock hatchery raised smelt in the LSZ. The agency-sponsored Delta Smelt conservation hatcheries could be upgraded to production status to provide juveniles to be stocked in the LSZ in late spring and summer. The population is so low now (zero 20-mm and Townet survey indices) that stocking would be helpful if not necessary.
  4. Provide a spring pulse flow into and through the Delta to help smelt fry transport from freshwater spawning areas downstream to the LSZ. This could include passing some Sacramento River flow through the blocked entrance to the Deepwater Ship Channel at the Port of West Sacramento. Delta inflow pulses could be provided by reservoir releases coordinated with infrequent natural flow pulses through the Delta.
  5. Manage tidal flows and Delta hydrodynamics, as well as water quality, on a real time basis to help maintain the LSZ in east Suisun Bay and to stimulate and sustain plankton blooms. Real time management is possible because of the many satellite-accessible data recorders in the Delta, as well as the many frequent biological monitoring surveys being conducted throughout the Bay and Delta. Active adaptive management is possible with the many flow controls available on diversions, reservoir releases, and flow splits (e.g., Delta Cross Channel).