Category Archives: Bay-Delta

Some Delta Smelt Back in the Delta

Posted on by

The US Fish and Wildlife Service’s early winter survey1 recently detected the first adult Delta Smelt of the water year in the Delta at Jersey Point on the lower San Joaquin River (Figure 1). The number collected in the survey through December 15th is 3, compared to 26 for the same period last year. Their appearance is on schedule and likely related to the first storm flow of the winter (Figures 2 and 3), and the freshening of the Delta (Figure 4).

Table of Smelt Count

Figure 1. Catch of adult Delta Smelt in early warning survey at two lower San Joaquin River stations in December 2015.

Graph of Delta freshwater outflow in December 2015

Figure 2. Delta freshwater outflow in December 2015. (Source: CDEC)

Graph of Turbidity of water at Jersey Point in December 2015

Figure 3. Turbidity of water at Jersey Pt in December 2015. (Source: CDEC)

Graph of Salinity (EC) at Jersey Point in December 2015

Figure 4. Salinity (EC) at Jersey Pt in December 2015. (Source: CDEC)

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. ↩

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

Posted on by

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.

Trap and Haul –a better Central Valley option

Posted on by

Last month, CalTrout’s blog had a post on a federal government program to trap-and-haul salmon and move them upstream of Shasta Reservoir.1 Earlier we also commented on trap-and-haul (http://calsport.org/fisheriesblog/?p=334). The National Marine Fisheries Service’s (NMFS) Recovery Plan for Central Valley Salmon and Steelhead prescribes trap-and-haul, as does their biological opinion for operation of state and federal Central Valley water projects.

Transporting adult salmon above dams and the offspring back below the dams is an expensive and difficult task. No one loves trap-and-haul, but NMFS considers it necessary to ensure that endangered salmon and steelhead do not go extinct. The prescription comes out of frustration that the populations are declining below the dams. Given the choice of extinction or doing something that no one is thrilled with, NMFS has chosen a set of actions in the latter category. The feds have again begun raising Winter Run Chinook in the fish zoo at Livingston Stone Hatchery to ensure there is some genetically pure stock available in the future. Having a wild stock above Shasta in the McCloud River seems a wiser option, given that those fish would be wild even if they spend some time in a truck. It is a further hedge against conditions like the past two years when the Bureau of Reclamation failed to keep their promise to protect the Winter Run downstream of Shasta.

NMFS has also prescribed trap-and-haul to pass Spring Run Chinook and Steelhead around Shasta Reservoir and other Central Valley dams. Stakeholders on the Yuba are developing a plan to carry out the prescription.

In a second blog post, CalTrout recently asked: “Will winter run go the way of the bull trout?”2 Most assuredly, trap-and-haul can help maintain populations while we get our act together below the dams. It’s a better option than a zoo.

Save the Winter Run Salmon

Posted on by

By now most everyone has seen the newspaper articles on the catastrophic decline in Winter Run Chinook salmon production in the Sacramento River below Shasta Reservoir in 2015. The number of Winter Run juveniles passing downstream past Red Bluff is down substantially from last year, when the estimated survival rate was 5%.  Many blame the drought  – the fourth year of drought.  I have blamed poor water management and the weakening of water quality standards prescribed to protect the salmon (see previous posts).

It is now time for extreme actions to save these fish.  This coming year’s winter adult run will be made up primarily of the 2013 spawn, with some from 2012.  These spawns were marginally successful and could produce enough spawners next summer to help fix this debacle.

The responsible agencies plan to take more eggs and increase smolt production at the Livingston Stone Hatchery near Redding.  They also plan to truck these hatchery smolts to the Bay to maximize their survival.  They will likely severely limit commercial and recreational fisheries that may harvest Winter Run.  They plan to again start raising a rescue population in captivity to ensure they have some fish in the future to draw on for recovery.  A new drought plan will again address how flows and water temperatures will be managed below Shasta.  The State Board may resist weakening Sacramento River and Delta water quality standards designed to protect Winter Run, unlike what they did in the last two years.  All of these actions together will indeed help Winter Run from further decline, but it will not be enough even if the El Niño brings abundant rain and snow.

What else?  The answer to that question should be everything that is reasonably possible to increase production and survival.  Here are some suggestions:

  1. Do not weaken Sacramento River and Delta water quality standards that protect Winter Run. (This alone would have averted the catastrophes below Shasta the past two years.)
  2. Minimize warm water inputs to the Sacramento River in summer from the Trinity River to keep Sacramento River temperatures lower and save Shasta’s cold-water pool.
  3. Alter peaking hydropower management and system infrastructure in Shasta-Trinity CVP system to improve water temperatures in the Sacramento River and the conservation of reservoir cold-water pools.
  4. Further limit Shasta-Trinity reservoir releases to water contractors to conserve cold-water pools and maintain flow requirements for salmon.
  5. Enhance natural winter and spring flow pulses from tributaries below Shasta with flow releases from Shasta to increase survival of emigrating wild juvenile salmon migrating downstream in the Sacramento River, to and through the Delta, and to and through the Bay to the ocean.
  6. Conduct an aggressive rescue program of adult Winter Run that migrate into Sacramento Valley bypasses only to be blocked below overflow weirs, or that migrate into dead-end basins, or that stray into other tributaries including Battle Creek, Feather River, and American River salmon hatcheries.
  7. Capture wild juvenile Winter Run in an enhanced trapping program at fish screen bypasses, screw traps, and other techniques in the Sacramento River in fall and winter migration period, and transport these juveniles to the Bay to avoid lower river and Delta sources of mortality.
  8. Modify Delta operations to maximize juvenile Winter Run survival through the Delta. This may involve further changes to Delta Cross Channel operations and Delta export schedules, as well as Delta inflow and outflow.
  9. Maximize egg taking and rearing capacity in hatchery system.
  10. Barge wild and hatchery young from the Sacramento River through the Delta for release in the Bay to avoid future straying problems associated with trucking fish.
  11. Raise juvenile hatchery salmon in floodplain habitats in winter in the Sacramento Valley (e.g., Sutter and Yolo Bypasses).
  12. Conduct egg injection or fry releases in appropriate locations in Battle Creek to jumpstart its prescribed new population; this can be managed at the Battle Creek hatchery.
  13. Develop and implement an emergency comprehensive plan with appropriate agencies with the necessary authority to carry out these actions. Include stakeholders in the plan development and review process.  Obtain necessary funding from available sources.