Federal Bay-Delta Biological Opinions Threaten the Survival of Bay-Delta Salmon Runs and California’s Salmon Fishing Industry

On October 22 the National Marine Fisheries Service released a biological opinion (BO) under the federal Endangered Species Act designed to authorize a dramatic increase in pumping from the Bay-Delta ecosystem by the Bureau of Reclamation’s Central Valley Project (CVP) – the largest water project in the nation. That Bay-Delta BO lays out rules related to winter and spring-run Chinook salmon, Central Valley steelhead and green sturgeon, all of which are listed under the federal ESA. The Fish and Wildlife Service also released a related BO regarding the listed delta smelt.

Threatening the Survival of Salmon Runs and the Salmon Fishing Industry: The new NMFS BO weakens every important constraint on CVP dams and pumps included in the current NMFS BO, which was released in 2009. If implemented, this new BO will cause severe damage to the Bay-Delta estuary, Central Valley rivers, all four Bay-Delta Chinook salmon runs, and to the jobs and communities that depend on those salmon. The new NMFS BO is a plan to cause salmon extinctions and to devastate fishing jobs.

Two decades ago, in 2004 and 2005, similarly politically manipulated BOs allowed record water pumping from the Bay-Delta. Those BOs led to a collapse of California salmon populations and the first ever closure of California’s Chinook salmon fishery in 2008 and 2009 – costing thousands of jobs and causing devastating impacts to fishing families and communities. Those BOs were invalidated by federal courts. In response to the court’s ruling, new BOs were adopted in 2008 and 2009. The new October 22 BOs would replace the 2008/2009 BOs. These new BOs could allow impacts as serious as – or even more serious than – the old invalidated BOs.

In its analysis, the Bureau of Reclamation concluded that new, weaker BO rules could increase Delta pumping by more than 600,000 acre-feet. Delta diversions during the peak salmon outmigration months of April and May would increase by an average of more than 350,000 AF. The Bureau also concluded that this proposal would:

• Increase dry year CVP Delta exports in the critical spring period by as much as 100 percent. (BA, Figure 53-5.)
• Increase above normal year exports during the spring by as much as 200%. (BA, Figure 53-3.)
• Increase average exports during spring months by 100%. (BA, Figure 53-1.)

In addition, because actual CVP operations would be authorized to be more aggressive than the Bureau’s modeling assumptions, actual exports – and impacts – could be even greater.

You Can Smell the Swamp from Here – Political Manipulation Produced the BOs: The new NMFS and FWS BOs are the result of sustained political manipulation, particularly by Secretary David Bernhardt, who formerly lobbied and litigated against the 2008 and 2009 BOs on behalf of the Westlands Water District.

The process of writing new Bay-Delta BOs began in 2016, when then-Interior Secretary Jewell acknowledged that the 2008 and 2009 BOs were inadequate, particularly because they failed to prevent a dramatic collapse of Bay-Delta fish species during the recent drought. Secretary Jewell also stated that new ESA BOs should provide protections stronger than those adopted in the 2008/2009 BOs. However, the new BOs dramatically weaken critical constraints on water diversions contained in those previous BOs. The reason for this decision is clear – President Trump told supporters in the arid western San Joaquin Valley that he would increase pumping, and Secretary Bernhardt is ignoring the law and science to deliver on that promise.

To their credit, dozens of NMFS scientists resisted this proposal to increase pumping. The first draft of the new BO, issued in July, found that the proposed increase in CVP pumping would threaten the survival of salmon and even the struggling southern resident orca population, which depends on salmon along the California and Oregon coast. Under Secretary Bernhardt’s supervision, that draft was thrown out and dozens of scientists were reassigned. Interior then appointed the Bureau of Reclamation to the team with the authority to write the final NMFS and FWS BOs for the CVP. The new, politically-driven conclusion – increasing pumping would not threaten the survival of ESA listed fish.

Aiming for Salmon Collapse: Overall, the biological opinion admits that, “reductions in the survival and productivity of all CV Chinook salmon populations (including fall-run and late fall-run Chinook salmon) are expected to occur throughout the proposed action, and the greatest effects will occur during the drier water years when effects of the proposed action are most pronounced.” (P. 683.) The increased dry year impacts are particularly damaging, in light of the devastating impacts on salmon during the last drought that were among the key reasons why Secretary Jewell called for stronger BOs in 2016.

Evidence of these anticipated impacts are clear throughout the document.

• The abundance of endangered winter-run Chinook salmon is 97% likely to be lower than under the 2009 NMFS BO (P. 696-697.)
• There is a higher risk of large population declines that threaten extinction than under the 2009 NMFS BO (P. 706-707.)
• In all months during non-wet years, survival of juvenile upper Sacramento River winter run salmon (smolts) will be lower than under the 2009 NMFS BO (P. 700.) These lower survival rates reflect differences in flow conditions in the Delta under the new BOs (P. 702.)
• Survival of juvenile salmon through the Delta in November is projected to decline from 45% under the 2009 NMFS BO to 30% under the new BO, as a result of more damaging operation of the Delta Cross Channel. (P. 390.) “Based on the result of the modeling for the October and November period, the proposed action will decrease through-Delta survival compared to the current operating scenario.” (P. 402.)
• The BO projects increases in the number of juvenile salmon entrained by the Delta pumps in all year types, including winter-run Chinook salmon (P. 489), spring-run Chinook salmon (doubling take in most water year type) (P. 500), and steelhead (increases take by percentages ranging from 15% to 38%) (P. 509-510.) Increased entrainment is anticipated to result in decreased migratory success for winter-run and spring-run Chinook salmon because the entrained fish are less likely to escape the influence of the Delta pumps (P. 497 and 506.)

Gutting Sacramento River Temperature Protections: Sacramento River basin salmon runs are the backbone of the California salmon fishing industry. The new BO allows the CVP to kill 100% of endangered upper Sacramento River winter-run salmon eggs and fry for three years running – before exceeding the authorized level of take (P. 801.) (The process of writing the new BO took three years and included no interim temperature protection actions. A similar three-year reconsultation process in the future could mean that the CVP could kill 100% of baby winter run salmon for 6 years running before new protections would be in place.) Given that most Chinook salmon live for three years, this new BO would allow the CVP operations to effectively extirpate wild winter-run salmon before stronger protections are even considered. Fall-run and late fall-run Chinook salmon could suffer similar damage, if cold water is not retained in Shasta Dam.

The new BO eliminates key temperature protections included in the 2009 NMFS BO:

• Eliminates any specific year-to-year water storage requirement to ensure adequate temperatures to allow salmon eggs and baby salmon to survive. This key deletion allows the CVP to drain water from Shasta to deliver to water contractors during the irrigation season at the expense of ensuring that enough cold water will be available the following year to protect salmon eggs and baby salmon.
• Eliminates the requirement that NMFS approve an annual plan for Shasta temperature operations before the CVP makes water allocation announcements.
• Eliminates monthly consultations with NMFS to ensure adequate temperature protection.

The elimination of specific protections and regular oversight by NMFS is clearly inappropriate because the CVP operations to contractors caused dramatic temperature impacts to salmon during the past drought. In 2014 and 2015, CVP operations drained the cold water in Shasta Reservoir, causing lethal temperatures that killed 96% and 97% of endangered juvenile winter run Chinook salmon in the Sacramento River (P. 69.) The current ESA rules are too weak to prevent these regular kills of baby salmon. But at least the carryover storage requirements of the 2009 BO helped ensure maintenance of a “cold water pool” behind Shasta Dam. Under the new BO, that requirement is eliminated. The fish kills in 2008 and 2009 were seen as a disaster by fisheries agencies at the time. However, identical fish kills may be allowed under the new BO.

Weakening or Eliminating Limits on Delta Pumping: The new NMFS BO dramatically weakens pumping constraints in the Delta.

• Eliminates the Inflow to Export ratio in the 2009 BO that limited the percentage of San Joaquin River flow into the Delta that can be diverted by the CVP and SWP Delta pumps (2009 BO, P. 641.)
• Allows increased Delta pumping that results in Old and Middle River flows more negative than -5,000 cubic feet per second (cfs) during storm events, with no limit on the magnitude, duration, or frequency of these increases. (P. 479.) Generally, limits under the 2009 BO are -2,500 cfs to -5,000 cfs (2009 BO, P. 648.)
• Nearly doubles the total number of steelhead allowed to be taken at the pumps in a single year from 3,000 in the 2009 NMFS BO (2009 BO, P. 776) to 5,800 (P. 810.)
• Reduces limitations on the Delta Cross Channel gates. When these gates are open, juvenile salmon are at far greater risk of being killed by the CVP pumps (P. 59.)
• Weakens the Fall X2 action in the 2009 FWS BO.
• Eliminates any ongoing authority for NMFS to respond to unanticipated fish kills caused by the CVP.
Eliminating Protections on Other Important Salmon Streams: The BOs also eliminate important protections for salmon on the Stanislaus River, the American River and Clear Creek. In addition, the BO fails to analyze the impacts of CVP operations on salmon in the Trinity River (BO, P. 5.)
Including a Shasta Dam Raise: The BO includes a damaging proposal to raise Shasta Dam despite the fact that “There are no operational scenarios in the BA to evaluate to confirm beneficial or adverse effects of a raised Shasta Dam and NMFS therefore cannot further evaluate the Shasta Dam raise in this opinion.” (P. 203.) The FWS BO also assumes that Shasta Dam will be raised (FWS BO P. 30.) This project is prohibited by state law. Federal scientists have previously found that this dam raise would cause serious impacts to salmon.

Eliminating Salmon Reintroduction Efforts: CVP dams blocks access to more California salmon spawning habitat than any other project, including blocking salmon spawning on the American, Stanislaus, San Joaquin, Sacramento and Trinity Rivers. The 2009 BO included a requirement regarding restoration of winter run Chinook salmon to Sacramento River tributaries above Shasta dam. This reintroduction project is critically important to the Winnemem Wintu tribe, for whom salmon play an important cultural and religious role. (The tribe lost much of their homeland, along with the winter-run salmon, when Shasta Dam was built.) The 2009 BO also included a reintroduction evaluation and implementation program on Battle creek (2009 BO, P. 603) as well as on the American and Stanislaus Rivers (2009 BO, P. 671.) The new BO eliminates all of those reintroduction requirements, replacing them with a $14.5 million contribution to the restoration of Battle Creek (P. 55) – with no performance milestones or deadlines. In short, the new BO does not require any salmon reintroduction effort to be implemented.

Phony Science: The new BO ignores the overwhelming scientific evidence compiled by the State Water Resources Control Board, the San Francisco Estuary Institute and others regarding the damage caused by current levels of water diversions and the need for increased – not decreased – Delta outflow.
For example, the State Board’s evaluation of the flow needs of the Bay-Delta ecosystem concluded that: “(r)ecent Delta flows are insufficient to support native Delta fishes.” And in its summary of scientific evidence supporting stronger flow requirements, the Board concluded that: “multiple aquatic species in the Bay‐Delta estuary are in crisis. Recovery of native species will require both habitat restoration and increased flow in Central Valley tributaries and the Delta.”
In addition, SFEI found that “(f)reshwater flows control the quality and quantity of estuarine habitat, support key ecological processes, and significantly affect the abundance and survival of estuarine biota, from tiny planktonic plants and animals to shrimp and fish”, and that “(f)reshwater flows to the San Francisco Estuary have continued to decline in amount and variability, creating persistent artificial drought conditions.”

Finally, the BO gives the Bureau of Reclamation authority to control future evaluations of the damage to salmon and other wildlife caused by CVP operations (P. 56) and risk assessments regarding the take of fish in the Delta (P. 60.) Given the Bureau’s long-standing disregard for science in the operations of the CVP, this is a clear case of the fox guarding the henhouse.

Nov. 27, 2019