Category Archives: Bay-Delta

NMFS on Salmon and the Drought, Part 2

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As noted in the first blog of this series, the National Marine Fisheries Service (NMFS) is responsible under the Endangered Species Act for protecting the endangered Winter Run Chinook salmon of the Sacramento River. But when the US Bureau of Reclamation (USBR or Bureau) and the Department of Water Resources (DWR) have asked NMFS to comment on proposed changes in Central Valley Project operations during the present four-year drought, NMFS has consistently concurred, often going against its own previous prescriptions and advice. As a consequence, the Winter Run salmon were put at great risk, decimating the 2014 and 2015 year classes and again placing the population at the brink of extinction.

April 8, 2014 Drought Operations Plan

On April 8, 2014, the Bureau and DWR issued a 2014 Drought Operations Plan, in which they proposed low releases in the Sacramento River in April and May:

Keswick releases will be held to no greater than 3,250 cfs, or as determined necessary to reasonably target no more than 4,000 cfs at Wilkins Slough, unless necessary to meet nondiscretionary obligations or legal requirements;

The critical phrase here is “nondiscretionary obligations.” It is the view of NMFS, as described in its Biological Opinion for the Operation of the State Water Project and Central Valley Project, that the Bureau of Reclamation does not have the discretion to release less water to Sacramento River Settlement Contractors than 75% of contracted amounts. Thus, low April and May flows called for in the 2014 Drought Operations Plan were overwhelmed by calls for water by the Settlement Contractors.

April 8, 2014 NMFS Letter on Sacramento River Water Temperature Management

On April 8, 2014, NMFS wrote a letter1 to the Bureau and DWR in response to their April 8, 2014 Drought Operations Plan. In that letter, NMFS concurred with the Plan, but highlighted a concern regarding deliveries to the Settlement Contractors:

“Winter-run Chinook salmon viability and Sacramento Settlement Contractor deliveries: Reclamation is working with Sacramento River Settlement Contractors on options to shift a significant portion of their diversions this year out of the April and May period and into the time frame where Keswick releases are higher to achieve temperature objectives on the upper Sacramento River. The willingness and cooperation of the settlement contractors in this effort would allow a modified diversion pattern and create the benefit of increased Shasta Reservoir storage at the beginning of the temperature control operations and increased availability of water to these senior water rights holders in this critically-dry year. This deferral of irrigation would allow implementation closer to the lower range of the Keswick release schedule for April and May, as identified in Section V of the DOP (Drought Operations Plan).

Thus the agencies and the Settlement Contractors were left to work out on a voluntary basis a mechanism to keep enough cold water in Lake Shasta to protect Winter Run salmon throughout the summer and fall. The State Water Board approved the Plan.

It didn’t work. Though releases from Shasta in April, 2014 were low, the Bureau ramped up releases from Shasta to the Settlement Contractors in early May (Figures 1 and 2), and cold water in Lake Shasta was depleted by the end of August.

Graph of May 2014 releases from Keswick

Figure 1. May 2014 releases from Keswick to the Settlement Contractors were far above those advised by NMFS (

Graph of releases May 2014

Figure 2. May 2014 releases from Keswick to the Sacramento River were diverted by Settlement Contractors upstream of the Delta. Contrast flow at Wilkins Slough (~25 miles north of Woodland) with releases from Keswick in Figure 1: most flow increases over the month were diverted north of the Delta.

January 29, 2015 Letter on Sacramento River Water Temperature Management

On January 29, 2015, NMFS wrote a letter to the Bureau and DWR in response to a new January Temporary Urgency Change Petition (TUCP) to the State Board.2 In its January 29, 2015 letter, NMFS’s acknowledged lessons from 2014 regarding water temperature:

Temperature management is critical. Salmon rely on cold water, particularly during early life stages when fish are young and vulnerable. Shasta and Keswick dams block endangered winter-run Chinook from accessing their native cold water habitat in the Upper Sacramento and McCloud Rivers, so their eggs and fry are particularly vulnerable to high summer temperatures. Data from the Sacramento River indicate 2014 temperatures were at levels that impact the survival of juvenile salmon and steelhead. We found that the 2014 temperature criterion was exceeded starting in August, resulting in approximately 95% mortality of eggs and fry upstream of Red Bluff Diversion Dam. As of December 16, 2014, an estimated 390,000 juvenile winter-run Chinook salmon passed Red Bluff, compared to 1.8 million in the previous brood year and 850,000 in brood year 2011, the year of the winter-run collapse (see Nov. 18 USFWS/CDFW/NOAA Fisheries presentation to State Water Board). This is the fewest winter-run Chinook juveniles per female spawner passing Red Bluff in 11 years.

March 27, 2015 Letter

However, by the end of March, 2015, NMFS was once again tiptoeing through a proposal by the Bureau to repeat the previous year’s disaster. On March 27, 2015 NMFS once again concurred with the proposed TUCP, even while highlighting the “conflict” between Winter Run salmon and deliveries to the Settlement Contractors. 3

The Project Description meets all of the required aspects of the contingency plan required in Action I.2.3 .C, as follows:

  • Reclamation has provided an assessment of additional technological or operational measures that can increase the ability to manage the cold water pool.
  • Reclamation notified the State Board, through filing the TUC Petition, that meeting the biological needs of winter-run and the needs of resident species in the Delta, delivery of water to nondiscretionary Sacramento Settlement Contractors, and Delta outflow requirements per D-1641 , may be in conflict in the coming season.
  • In conclusion, NMFS concurs that Reclamation’s Project Description is consistent with Action I.2.3.C and meets the specified criteria for a contingency plan. … Furthermore, the best available scientific and commercial data indicate that implementation of the interim contingency plan will not exceed levels of take anticipated for implementation of the RPA specified in the CVP/SWP Opinion.

And once again in 2015, no one stepped up to maintain cold water in Shasta Reservoir in April and May (Figure 3).

Graph of 2015 releases

Figure 3. In 2015, releases to the Settlement Contractors ramped up in April and were high throughout May.

July 1 Letter4

By July 1, 2015, NMFS was already issuing a post-mortem.

“NMFS acknowledges that storage in Shasta Reservoir at the beginning of the temperature management season in June, and the quantity and quality of the cold water pool, will not provide for suitable winter-run habitat needs throughout their egg and alevin incubation and fry rearing periods.”

Final Comment

We should expect more from the federal agency mandated to protect our endangered salmon. At a minimum, NMFS should have not concurred, in 2015 (or in 2014, for that matter), and should have called out the fact that added take of Winter Run would occur, further jeopardizing the viability of the species through direct mortality and degradation of their critical habitat.

Regardless of the legal merit of NMFS’s position that it does not have authority under the Endangered Act to limit deliveries to the Settlement Contractors, its failure to defend listed Winter Run gave cover to the Agency that has that authority: the State Water Board. CSPA, the Bay Institute and others asked the State Water Board in February, 2015 and again in the spring to reduce 2015 deliveries to the Sacramento Valley Settlement Contractors to save the Winter Run (and to protect Delta smelt). In an Order denying Petitions for Reconsideration of the 2015 TUCP’s filed by CSPA and others, the State Water Board offered the rationale:

However, at the time the changes were approved, the tradeoff appeared to be reasonable based on the information available at the time, including biological reviews from DWR and Reclamation and concurrence from the National Marine Fisheries Service (NMFS), U.S. Fish and Wildlife Service (USFWS), and California Department of Fish and Wildlife (DFW) (collectively fisheries agencies) with the changes. For these reasons, the petitions for reconsideration of the past Executive Director actions are denied. 5

NMFS on Salmon and the Drought, Part 1

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The National Marine Fisheries Service (NMFS) is responsible under the Endangered Species Act for protecting the endangered Winter Run Chinook salmon of the Sacramento River. But when the US Bureau of Reclamation (USBR or Bureau) and the Department of Water Resources (DWR) have asked NMFS to comment on proposed changes in Central Valley Project operations during the present four-year drought, NMFS has consistently concurred, often going against its own previous prescriptions and advice. As a consequence, the Winter Run salmon were put at great risk, decimating the 2014 and 2015 year classes and again placing the population at the brink of extinction.

January 29, 2015 Letter on Old and Middle River Flows

On January 29, 2015, NMFS wrote a letter in response to the Bureau and DWR’s January Temporary Urgency Change Petition (TUCP) to the State Board.1 The Petition asked the State Board to weaken State water quality standards. NMFS stated:

Here’s what we learned from monitoring salmon in 2014 that will inform our strategies for managing the drought in 2015:

1. Managing Old and Middle River (OMR) flow regimes to protect salmon is critically important. Effectively managing flow regimes allows juveniles to stay in the best habitat in the North Delta, ensuring they are not drawn toward the South Delta pumps where they are frequently killed by predators or the pumps themselves. During a rare rainstorm last March, and under a flexible operation approved as part of the 2014 Drought Contingency Plan, we allowed for higher levels of pumping and reverse OMR flows.  Evaluating the effects of the action this fall, we learned that salvage and loss of juvenile Chinook salmon, including winter-run, at the federal and state fish collection facilities increased when OMR’s 14-day running average was more negative than -5,000 cfs. This confirms the importance of managing OMR flows carefully to ensure pumping is increased when it will be most effective for increasing water supply and least impactful to juvenile fish.

Regardless of whatever NMFS had learned from events in 2014, NMFS had already ignored these lessons in December 2014 when it allowed OMRs to significantly exceed the -5000 cfs limit (Figure 1). NMFS then acquiesced to high reverse flows in the 2015 Drought Operations Plan: “OMR shall be no more negative than -5,000 cfs as a 14-day running average, and no more negative than -6,250 cfs as a 5-day running average, except as needed to capture sporadic storms (increase exports).”

The first winter storms usually trigger emigration of juvenile Winter Run and Late Fall Run Chinook salmon into and through the Delta (Figure 2). The only time during a drought that operators can achieve the highly negative OMR levels is in sporadic storms. Since those are precisely the conditions under which emigrating salmon pass through the Delta, the highly negative OMR flows put migrating juvenile salmon at great risk.

Figure 1. Old and Middle River flows in December 2014. Negative or reverse flows are caused by South Delta Exports, which reached over 10,000 during the second week of December 2014. (Data source: CDEC)

Figure 1. Old and Middle River flows in December 2014. Negative or reverse flows are caused by South Delta Exports, which reached over 10,000 during the second week of December 2014. (Data source: CDEC)

Graph of Occurrence of juvenile salmon

Figure 2. Occurrence of juvenile salmon in winter 2004 in seines and trawls near Sacramento at entrance to tidal Delta. Other years have shown a similar pattern. (Source: http://www.science.calwater.ca.gov/pdf/ewa/ support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf )

Some Delta Smelt Back in the Delta

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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

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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

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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.