Author Archives: Tom Cannon (with Chris Shutes)

Delta Fish and Flows – Listen to our fish scientists

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The Delta independent Science Board, made up mostly of non-Californians and non-fish biologists, waded into the fray on Delta issues again with their recent report:  Flows and Fishes in the Sacramento-San Joaquin Delta – Research Needs in Support of Adaptive Management 1

After 50 years of extensive research and adaptive management, the Delta water managers still believe we need the insights of outsiders before the secrets of the Delta are exposed to improve water management for fish.  Once the center of world-wide estuarine science beginning in the 60’s and 70’s, the San Francisco Bay Delta now has new advice sought from outside sources.  I came to the Bay-Delta in the late 70’s as an outsider to learn from and participate in comprehensive fish-ecosystem science going on in the Bay-Delta.  I was honored to participate in and contribute to Bay-Delta science.  Many of the young scientists who came with me then and since have contributed decades of their careers to Bay-Delta science.  Yet there is this continuing quest for more outside input fraught with non-fish science.

The Report

Delta Independant Science Board Report Cover

“The economic, ecological, and social costs of scientific uncertainty in water management controversies are significant – and to some degree unavoidable.  This report therefore recommends, first and foremost redoubling effects to identify causes and effects concerning fishes and flows in the Delta.”  (Page 5).  Uncertainty is not the cause of the failure in protecting the Bay-Delta ecosystem.  It is a failure to use science with its uncertainties to protect the ecosystem.  After 40-plus years of study, the answers are obvious.  Redoubling?  Why not simply recognizing the obvious?  There are no doubts that changes in flows are the cause of most of the Delta problems, and that changes designed to reduce entrainment of fish at the Delta export pumps (OMR, etc.) have proven ineffective.  There is no need to redouble efforts to understand the relationship between flows and fish.  We know why the Winter Run salmon were wiped out below Shasta in 2014 and 2015.  We know why Delta and Longfin Smelt populations have been at record lows the past two years.

“The habitat and flow needs of the native species are difficult to define in the transformed place and in a novel ecosystem.”  (Page 5).  The habitat and flow needs are well known.  The ecosystem, though “transformed,” is not novel.  Anyone who has been here awhile and studied the fish knows.

“Focus on cause and effect – the mechanisms that enable flows to affect fishes.  Deeper causal understanding is important for identifying and reducing risks to water supply and fish populations.”  (Page 5).  We’ve been through this time after time.  Overwhelmingly, finding the political will to follow the science we already have is far more critical than fine-tuning the mechanistic understanding of how fish respond to flow.  The problem in the Delta is systemic: water management has turned the hydrograph on its head and deprived the estuary of half of its flow (in dry year sequences, more than half).  The State Water Board’s 2010 Delta Flow Criteria Report 2 got this fundamentally right: on a mass and systemic basis, Delta inflow and outflow need to be radically increased to provide basic system functions, including variability.   Not every effect is a direct effect.  Focusing only on direct effects – the “causal mechanisms” – is overwhelmingly about “risks to water supply.”  Beneath the surface of hunting for mechanisms is an engineering-style belief that one can surgically provide water to produce this or that benefit at the exact moment it’s needed.  Sure, better understanding is good, and different specific actions can help.  But the need isn’t met by adding up specific actions.  We need to restore underlying ecosystem function that serves as a foundation for targeted improvements.  Right now we aren’t even close.

“Understanding the dependencies of fishes on water flows is central to understanding the Delta ecosystem.  Relationships between fishes and flows drive state and federal policy and related regulatory and management decisions, and consequently have been central to legal arguments and decisions.”  (Page 9).  Delta water quality control plans, and water rights orders since the 1960s (mainly D-1485 and D-1641), have recognized (and focused) on the relationship between flows and fishes.  Earlier, the focus was on striped bass and flows (D-1485), but more recently the focus has been on smelt-salmon and flows (D-1641).  There have been changes in summer standards that hurt striped bass while strengthening winter-spring standards have helped smelt and salmon.  But after decades of management under the standards and an array of biological opinions, it is obvious to most that the level of protections has been inadequate.  The problem is not a lack of science and understanding; it is a lack of commitment to them.

 “A comprehensive, integrative, and well-planned scientific approach focused on processes, drivers, and predictions is needed to aid near-term and long-term adaptive management and to predict how future changes might affect fishes.”  (Page 21). The Bay-Delta has had this for 50 years.  The science, data, and adaptive management are well documented, as well as reflected in water rights, water quality standards, biological opinions, and management and recovery plans.  But most important of all, they are carried in the minds of hundreds of Bay-Delta scientists who have dedicated their careers to this purpose.

 “The development of a generalized fish model portable for different fish species and for different water management decisions is needed to forecast  expected consequences and timelines for adaptive  management strategies.”  (Page 23). Such models already exist in many forms that reflect and carry the knowledge of what has been learned over the past 50 years.  Models developed in the 60’s for striped bass still work today.

Follow-up Workshop

At the follow-up Delta Independent Science Board workshop in December, Dr. Lund, chairman of the Science Board, discussed the major findings of the report, the first being that connecting flows and fishes is central to achieving the state’s coequal goals. “The modern Delta is not a native ecosystem but is dominated by non-native species with some natives, and that’s a particular challenge for some of the ecosystem goals for the Delta,” he said.  “Statistical analyses show that flows do affect fish, but decisions need a little bit more causal understanding of how flows involve fishes, especially as we try to manage the Delta and make some larger changes over time. Where larger changes occur in the Delta that we have to respond to, we need a more causal understanding of how these relationships work.”3  In my experience, when correlations that support science theory continue becoming more statistically significant with each added year of data, it is time to accept the theories and start doing something.  Using the same excuses for inaction and continuing to promote more science will not save the Bay-Delta ecosystem.

In Conclusion

What has been missing for decades is this:  our locally grown fisheries scientists have no access to what are often called the “knobs” of management in the Delta.  Instead of scientists, resource agency managers and water purveyors constrict the range of adaptation to protect water supply at the expense of fishes and their habitats.  Adaptive management is driven by managers.  Our Smelt and Salmon Working Groups are stymied by senior management and by political oversight and control.  Adaptive management in the Delta has become a synonym for how far fisheries agency managers will agree to weaken resource protection.  Examples include weakening water quality standards in droughts; allowing unrestricted water transfers through the Delta; and closing the Delta Cross Channel gates in summer.

It is time to listen to our home-grown fish scientists and let them turn the knobs in the right direction.

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 )

Trap and Haul and Reservoir Populations of Chinook Salmon

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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.