Trump’s Bay-Delta Biops Are a Plan for Extinction

Given the trail of environmental degradation, unlawful agency action, and scientific misconduct left in the wake of decision-making by the Trump Administration and Interior Secretary David Bernhardt, it’s no surprise that the new biological opinions for the Bay-Delta dramatically increase water diversions for Mr. Bernhardt’s former clients and dramatically weaken or eliminate protections for salmon and other endangered species. As we continue to read through the biological opinions, here are detailed reasons why these biological opinions are a plan for extinction in the Bay-Delta.  

The New Biological Opinions Weaken or Eliminate Many of the Requirements in the 2008 and 2009 Biological Opinions

The final biological opinions issued by FWS and NMFS in October 2019 weaken or eliminate many of the specific protections for endangered species required under the 2008 and 2009 biological opinions, including:

Shasta Dam operations:

  • Eliminating requirements for carryover storage in Shasta Dam, which helps ensure adequate cold water for the following year (NMFS RPA Action I.2);
  • Eliminating requirements that NMFS approve an annual plan for Shasta water temperatures to protect salmon prior to USBR announcing water supply allocations in February, with monthly consultations between NMFS and USBR to ensure they maintain adequate cold water for salmon (NMFS RPA Actions 1.2.3 and 1.2.4);
  • Eliminating program to evaluate and enable reintroduction of winter-run Chinook salmon above Shasta Dam (NMFS RPA Action 1.2.5).

Delta operations:

  • Allowing Delta pumping that results in Old and Middle River flows that are more negative than -5,000 cfs during storm events between January and June, with no limit on the magnitude, duration, or frequency of such OMR storm “flexibility” events (Overriding RPA Action IV.2.3 in the 2009 NMFS biop and RPA Actions 1, 2, and 3 in the 2008 FWS biop);
  • Eliminating the San Joaquin River inflow: export ratio, which regulates Delta pumping during the months of April and May, in the NMFS biological opinion (NMFS RPA Action IV.2.1);
  • Weakening the Fall X2 action in the FWS biological opinion by reducing the minimum Delta outflow required to protect Delta Smelt (RPA Action 5 in the FWS biop).

Clear Creek operations:

  • Eliminating requirements to meet maximum water temperatures in dry and critically dry years that protect salmon and steelhead (NMFS RPA Action I.1.5).

Stanislaus River operations:

  • Reducing the minimum instream flows on the Stanislaus River that NMFS required to protect steelhead (NMFS RPA Action 3.1.3);
  • Eliminating NMFS’ requirement to manage water temperatures to protect spawning and rearing steelhead (NMFS RPA Action 3.1.2).

There are many more examples of specific protective measures in the current biological opinions that these new opinions weaken or eliminate, and all (or nearly all) of the habitat restoration and other measures included in these new biological opinions, including restoration of Battle Creek or Yolo Bypass restoration, were already required to be implemented under the 2008 and 2009 biological opinions.  

And in far too many cases, protective measures in these new biological opinions are not reasonably certain to occur. For instance:

  • Reductions in Delta pumping to reduce reverse flows in Old and Middle River to -3,500 cfs are not mandatory even after cumulative salvage limits are hit (see the final Biological Assessment (“BA”) at 4-70); and
  • The fall outflow action in the Delta Smelt biological opinion may not be fully implemented, or implemented at all (see FWS biological opinion at 53, 164, 165).

In addition to weakening existing protective requirements, the new biological opinions also weaken the decision-making process: they generally eliminate the mandatory authority of NMFS and FWS over real-time operations, so that the Bureau of Reclamation can go back to ignoring the recommendations from fishery biologists—as they did in the early 2000s, prior to the 2008 and 2009 biological opinions. Overall, there’s no question that these new biological opinions dramatically weaken or eliminate existing protections for salmon and other endangered species in the Bay-Delta watershed.

State and Federal Agencies Previously Concluded that the 2008 and 2009 Biological Opinions Needed to Be Strengthened to Avoid Extinction

Prior to Trump’s election, state and federal agencies were clear that they were revising the 2008 and 2009 biological opinions in order to strengthen them, as greater protections were needed to prevent extinction. Most notably, in 2016 Secretary of the Interior Sally Jewell concluded that, “The reinitiation process will likely lead to new or amended biological opinions that will increase protections for these species,” warning that the efforts to could lead to further reductions in water supply. Similarly, in January 2017 NMFS concluded that the existing protections for salmon below Shasta Dam were inadequate, and proposed amendments to the Shasta RPA in the 2009 biological opinion to significantly strengthen water temperature protections. 

Yet rather than strengthening protections, the new biological opinions dramatically weaken protections. The independent scientific peer reviews of these biological opinions recognized the lack of reasoned explanation between the fact that the species have been declining over the past decade and the agencies’ conclusions that weakening existing protections would not jeopardize the species. For instance, one of the independent scientific peer reviewers noted that, “… it seems the overall logic in the BiOp is COS is part of baseline and the with COS the populations have been declining. Therefore, if PA has similar effects as COS, then the populations will continue on their trajectories.” Similarly, another of the independent peer reviewers noted that, “Two observations stand out in the current BiOp: (1) Delta Smelt abundance is the lowest ever observed and is expected to continue to decline, and (2) the Proposed Action includes an annual increase in water exports from the ecosystem.”  

Appendix 1 to the Delta Smelt biological opinion (Figure 7) shows that even without weakening protections for Delta Smelt, the population—which is nearly extinct—is anticipated to decline 70% over the next decade:

The Process of Developing These Biological Opinions Was Tainted by Political Interference from Start to Finish

The process of developing these biological opinions has been replete with examples of improper political interference.

Although the biological opinions were supposed to result in stronger protections, things apparently changed with Trump’s election and appointment of David Bernhardt at the Interior Department. Mr. Bernhardt personally intervened in the reinitiation of consultation process in November 2017, despite his conflicts of interest due to his prior work as a lobbyist and lawyer for the Westlands Water District, on whose behalf he had unsuccessfully sued to overturn these biological opinions and unsuccessfully lobbied Congress to override or preempt these biological opinions. As a result of Mr. Bernhardt’s interference, in December 2017 the Bureau of Reclamation formally announced that the purpose and need for this action under NEPA was “maximizing water deliveries.” This purpose and need statement is inconsistent with the need to strengthen protections for endangered species and is inconsistent with the Central Valley Project’s authorized purposes, as Congress has required that the CVP be operated to meet co-equal purposes of water supply and fisheries protection. 

Next, in October 2018 President Trump issued a memorandum that directed the agencies to identify and suspend regulations that burdened water supply, imposed a very short timeline for completing the biological opinions (despite concerns from the agencies that they had inadequate time and resources to adequately assess the impacts of operations on listed species), and directed that Paul Souza of the U.S. Fish and Wildlife Service manage the preparation of both the FWS and NMFS biological opinions. 

Finally, on July 1, 2019, scientists with the National Marine Fisheries Service concluded that the proposed operations would jeopardize listed salmon and violate the ESA, but the Trump Administration refused to sign the biological opinion. Instead, the Trump Administration replaced the team of scientists working on the biological opinion, in order to rewrite its conclusion, and a NMFS political appointee in Washington D.C. signed the final biological opinion (See page 1), which concluded that the proposed operations would not jeopardize listed species. 

What began as a process under President Obama to increase protections for endangered species ended under President Trump as a plan to increase water diversions for contractors and reduce protections for endangered species. The process under the Trump Administration appears to have been tainted from start to finish.

The Trump Biological Opinions Increase the Number of Endangered Species that Can Be Killed

Not only do these new biological opinions remove many of the protections required under the 2008 and 2009 biological opinions, but they also dramatically increase the number of endangered species that can lawfully be killed by the Central Valley Project and State Water Project (known as “incidental take”), including:

  • Allowing the Central Valley Project to legally kill 100% of the endangered winter-run Chinook salmon below Shasta Dam due to water temperatures in three consecutive years before reinitiation of consultation is required (NMFS BiOp, page 801). This means that high temperatures could result in extinction of winter-run Chinook salmon in the wild before reinitiation of consultation is required;
  • Increasing the number of juvenile steelhead that can be killed at the Delta pumps from salvage of 3,000 steelhead in a year in the 2009 NMFS biop to loss of 2,760 steelhead from December 1 to March 31 and 3,040 steelhead from April 1 to June 15 (NMFS biop, page 810), even though the maximum loss in the past decade under the 2009 NMFS biop was 2,852 steelhead (NMFS biop, page 508);
  • Eliminating all limits on the number of adult Delta Smelt that can be killed at the Delta pumps, and deferring to the future how to calculate a limit on the number of larval and juvenile Delta Smelt that can be killed at the pumps (FWS biop, pages 42-47) (this despite the fact that one of the independent scientific peer reviews (see page 35 of this document) concluded that the proposed approach to incidental take for larval Delta Smelt in the biop would likely lead to extinction);
  • Apparently increasing the number of endangered winter-run Chinook salmon that can be killed at the Delta pumps from 1% of the juvenile production estimate (2009 NMFS biop, for genetically identified fish) to 2% of the juvenile production estimate in any single year (NMFS Biop, page 810).    

The agencies also rely heavily on the use of surrogates for incidental take, often without a reasoned explanation or justification for the use of surrogates and/or without ensuring that the incidental take limits provide a clear indication of when reinitiation of consultation is required.

The Best Available Science Demonstrates that the Proposed Operations of the CVP and SWP Are Likely to Jeopardize the Continued Existence of Salmon and Delta Smelt

Although agency staff have publicly claimed that these biological opinions will be as protective as the 2008 and 2009 biological opinions, the modeling and analyses in the new biological opinions demonstrate that these measures will leave salmon and other endangered species worse off than under than the 2008/2009 biological opinions. For instance, the results of the Winter Run Life Cycle Model in the NMFS biological opinion show that under the new biological opinions:

  • The abundance of endangered winter-run Chinook salmon will be lower than under the 2009 NMFS biological opinion (NMFS Biop, page 696);
  • Survival of juvenile winter-run Chinook salmon migrating through the Delta will be lower than under the 2009 NMFS biological opinion (NMFS Biop, pages 702-703); and
  • There is a higher risk of large population declines that threaten extinction than under the 2009 NMFS biop (NMFS Biop, page 707).

The IOS life cycle model predicts that through Delta survival for winter-run Chinook salmon will be slightly higher, and abundance slightly higher, than under the 2009 biological opinion—but it predicts that the population will decline significantly under both biological opinions, from a starting population of 5,000 down to a median adult escapement of 3,864 (2009 biop) or 3,909 (NMFS biop). (NMFS biop, 691-694)

The other models and analyses used in the biological opinion find that operations under the new biological opinions are anticipated to reduce survival of salmon migrating through the Delta, including:

  • Perry Survival Model: reduced through Delta survival of winter-run and yearling spring-run (NMFS Biop, page 402);
  • Delta Passage Model: reductions in survival through the Delta for winter-run Chinook salmon (NMFS Biop, page 382), spring-run Chinook salmon (1.4%: pages 382-83), fall-run Chinook salmon (1.1%: page 383), and late-fall run Chinook salmon (page 383-84). 

And the modeling in the NMFS biological opinion shows that it is expected to increase the number of juvenile salmon that are entrained by the Delta pumps, including winter-run Chinook salmon (page 489), spring-run Chinook salmon (nearly doubling take in most years, see page 500), and steelhead (page 509-510). 

Overall, the biological opinion admits that, “Based on the analyses of expected effects of the proposed action to ESA-listed CV Chinook salmon populations, 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.” (NMFS biop, page 683)

Even as the biological opinions show that they will worsen conditions for endangered salmon and other species, it’s clear that simply maintaining the status quo under the prior biological opinions was not adequate to provide the conditions needed to prevent extinction. Indeed, NMFS’ recovery plan finds that significant increases in survival through the Delta—not further reductions in survival—is necessary for winter run Chinook salmon and other salmon species to recover (see page 127 of the final recovery plan). But most damningly, NMFS has repeatedly found that dramatically increased protections below Shasta Dam are needed to protect salmon, and yet the final biological opinion fails to provide the protections that NMFS has previously found was needed.

For instance, in 2017 NMFS proposed an amendment to the 2009 biological opinion to strengthen water temperature protections below Shasta Dam, including maximum mortality levels by water year type. Modeling in the BA shows that the 2019 NMFS biological opinion would result in mortality that is twice the levels proposed by NMFS in 2017:

Water Year Type

Temperature Dependent Mortality – 2017 Shasta RPA Amendment

(page 217 of the pdf)

Temperature Dependent Mortality: 2019 Final Biological Assessment Modeling

(page 1792 of the pdf)

Wet

Less than 3%

5%

Above normal

Less than 3%

4%

Below Normal

Less than 3%

11%

Dry

Less than 8%

10%

Critical

Less than 30%

61%

Similarly, in July 2019 NMFS scientists concluded that the proposed project would jeopardize listed salmonids, and proposed a reasonable and prudent alternative that included limits on temperature mortality below Shasta Dam that are dramatically stronger than the protections anticipated (but not required) under final biological opinion:

July 2019 NMFS Jeopardy Biological Opinion

(See page 945)

Final NMFS Biological Opinion

(See page 802)

Tier 1

Required frequency of years

At least 2 out of 3 years

None required

Maximum temperature dependent mortality

2%

15% in two consecutive years (Take would be exceeded if, in 2 consecutive years, temperature dependent mortality exceeds 15% and egg to fry survival is less than 29%)

Minimum egg to fry survival

32%

29% in two consecutive years (see above)

Tier 2

Required frequency of years

No more than 1 out of 4 years

None required

Maximum temperature dependent mortality

12%

31% in two consecutive years (Take would be exceeded if, in 2 consecutive years, temperature dependent mortality exceeds 31% and egg to fry survival is less than 21%)

Minimum egg to fry survival

27%

21% in two consecutive years (see above)

Tier 3

Required frequency of years

No more than 1 out of 4 years

None required

Maximum temperature dependent mortality

12%

65% in two consecutive years (take would be exceeded if, in 2 consecutive years, temperature dependent mortality exceeds 65% and egg to fry survival is less than 21%)

Minimum egg to fry survival

27%

21% in two consecutive years (see above)

Tier 4

Required frequency of years

No more than 1 out of 10 years

None required

Minimum egg to fry survival

Target 15%

“Two consecutive years of egg-to-fry survival of less than 15 percent followed by a third year of less than 21 percent based on fry production at Red Bluff Diversion Dam.” (page 801)

The final biological opinions fail to provide any explanation, let alone a reasoned explanation, why these higher levels of mortality below Shasta Dam would not jeopardize the species.

The Biological Opinions Underestimate Adverse Effects on the Species Because They Fail to Model or Analyze the Full Effects of the Proposed Action

The biological opinions are further problematic because they fail to model or analyze the actual project that was proposed, in ways that grossly underestimate the adverse effects of the proposal on fish and wildlife. In particular:

  • The biological opinions rely on modeling that assumes that water storage in Oroville Reservoir is drained far below dead pool in every major drought in order to meet water quality and water supply requirements, according to staff from the U.S. Fish and Wildlife Service. (see this email, this email and the attached spreadsheet) As a result, in a real drought the water projects would run out of water and could not operate as modeled, resulting in other protections for the species likely being waived, as they were in 2014 and 2015—causing devastating impacts to the species.
  • The biological opinions admit that they do not use the best scientific data on climate change, instead relying on modeling that underestimates the effects of increased air and water temperatures resulting from climate change, and which does not account for more frequent or more severe droughts from climate change. (See NMFS biop at 48, 51-52)
  • The biological opinions do not model or analyze the effects of meeting full contract deliveries for the Sacramento River Settlement Contractors, instead only analyzing the effects of meeting historic demands for water, which are significantly less than total contract amounts. (Final Biological Assessment at 4-11, footnote 1)
  • The biological opinions admit that even though the proposed project includes the operation of an enlarged Shasta Dam (notwithstanding the requirements of state law!), they fail to model or analyze the effects of this proposal: “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.” (NMFS biop at 203)
  • The biological opinions fail to model and analyze the effects of OMR storm flexibility authorized in the biological assessment. Instead, the biological opinions assume no OMR storm flexibility in wet years, one 7-day event at -6,000 cfs in January and February of Above Normal and Below Normal water year types, and one 7-day event at -6,000 cfs in either January or February of Dry water years. They also assume that salvage limits would have been reached in April, requiring -3,500 cfs OMR for April to June. (Final Biological Assessment, Appendix D, at pdf pages 36-37). As a result, the biological opinions never model or analyze the effects of an OMR storm waiver that is more negative than -6,000 cfs, that lasts longer than 7 days, or that occurs more than twice per year.  The modeling (see page 631 of Appendix D) and analyses assume very limited OMR storm flexibility, and more restrictive OMR thereafter, than is actually required by the biological opinions.
  • The biological opinions and biological assessment model the operations that were initially proposed in January. This modeling in the final biological assessment estimates that annual Delta exports would increase by nearly 500,000 acre feet on average, with most of that increase in pumping coming in the spring months (see Figure H2 here and page 822 of Appendix D).

The Trump Administration’s biological opinions fail to provide the measures needed to protect salmon and other threatened and endangered species, fail to use the best available science, and are a plan for extinction in the Bay-Delta.

About the Authors

Doug Obegi

Director, California River Restoration, Water Division, Nature Program

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