Share This!
Text SizeAAA Share Email

Salmon Experts Pressured to Change Findings

Michael Kelly, a former biologist with the National Marine Fisheries Service (NMFS), blew the whistle on political interference with his team’s April 2002 scientific findings on protections for the endangered coho salmon in the Klamath River basin. Other reports have indicated that President George W. Bush, Vice President Dick Cheney and presidential adviser Karl Rove all took an active interest in securing the diversion of water from the Klamath to local farmers for irrigation – leading to a conflict over Endangered Species Act (ESA) protections for the salmon. Following the manipulation of the NMFS biological opinion, water was diverted for agricultural purposes, and tens of thousands of fish died in one of the largest fish kills in recent history.


The Klamath River Basin, which flows to the Pacific Ocean from parts of southern Oregon and northern California, is home to three threatened and endangered species—the Lost River sucker,1 the shortnose sucker,2 and the coho salmon.3 The U.S. Bureau of Reclamation (BOR) operates the Klamath Basin Project, which is a system of dams and diversion structures that store and deliver water to agricultural users in the Upper Klamath Basin.4 Serving about 1,400 farms, the Klamath Project provides irrigation water for approximately 240,000 acres growing a variety of crops, such as wheat, potatoes, and alfalfa.5 Water rights are also retained by several Indian tribes that depend on the water and salmon populations for subsistence, and religious and cultural reasons.

Due to the presence of the three endangered species in the regions affected by the Project, the BOR must also take into account the ESA when setting its policies. Under Section 7 of the ESA, it is the responsibility of the BOR to determine (in a biological assessment) whether or not any proposed actions will adversely affect the threatened and endangered species whose habitat is in the Klamath River Basin.6 If the actions are found to jeopardize species, the BOR must then consult with NMFS7 and the U.S. Fish and Wildlife Service (FWS) to create a final biological opinion that proposes a “reasonable and prudent alternative” (RPA) to the initial plan.

The 2001 biological opinion (BiOp) conducted by the NMFS found that the ongoing operation of the Klamath Project is “likely to jeopardize the continued existence of SONCC coho salmon.”8 In 2001, the northwest region of the U.S was suffering from a severe drought.9 The especially dry conditions made it impossible for the Project to meet both its irrigation requirements and maintain river flows and lake levels sufficient for the coho salmon and suckerfish. Following the April 2001 BiOp, a judge ordered the BOR to ensure sufficient water flows to protect the fish and the BOR closed off the head gates to the irrigation canals that provided water to the farmers.

This decision sparked a massive public outcry including civil disobedience by farmers protesting the water cutoff. In one demonstration, protestors organized a symbolic 10,000 person bucket-brigade;10 in another protest, farmers forcibly opened irrigation canal head gates and released water downstream.11

High-Level Interest

Vice President Dick Cheney took a keen interest in the Klamath River situation. Shortly after President Bush’s inauguration, Cheney contacted Sue Ellen Wooldridge, the 19th-ranking Interior Department official who was in charge of the Klamath situation. His message explained, “This is Dick Cheney. I understand that you are the person handling this Klamath situation. Please call me at – hmm, I guess I don’t know my own number. I’m over at the White House.” Wooldridge initially thought that the voice mail message was a joke, but a follow-up call from an aide informed her that she was expected to keep Cheney’s office abreast of the situation on a weekly basis.12 Cheney, Wooldridge said, “was coming from the perspective that the farmers had to be able to farm -- that was his concern. The fact that the vice president was interested meant that everyone paid attention.”

President Bush also publicly supported diverting water to the farmers. At a January 2002 campaign event for Senator Gordon Smith (R-OR) Bush said, “We’ll do everything we can to make sure water is available for those who farm.” The next day, Karl Rove, Bush’s top political advisor, gave a general power point presentation during a retreat for 50 top managers at the Interior department. Included in the presentation was a slide about the water levels in the Klamath River basin. Rove expressed that the White House favored releasing water for irrigation.13

As a strategy for securing the release of the water, without invoking the emergency rules available under the ESA, Cheney hit upon the idea of scrutinizing the scientific basis for the 2001 BiOp by requesting a review of the science by the National Research Council (NRC) of the National Academies. Although, the official request for a NRC review came from the Department of the Interior, according to former congressman, Robert F. Smith (R-OR), Cheney contacted the National Academies directly to push for the review.14

The interim NRC report, released in March 2002, concluded that scientific evidence linking lake and river levels to the health of the sucker and coho salmon populations was lacking and that the RPA provisions regarding those aspects were not well-supported.15 Because the interim NRC report was released only four months after being commissioned, some biologists have criticized its scientific value. Douglas Markle and Michael S. Cooperman, experts on endangered suckers at Oregon State University, strongly criticized the NAS review for emphasizing simple connections in a highly complex ecosystem. The authors stated that the FWS’s original BiOp was “more rigorous, thorough, and defensible” than the Interim Report.16

In their final report, released in 2004, the NRC Panel stood by the conclusions of the interim report, but they also refused to criticize the science and reasoning in the original BiOp, stating: “The agencies can be expected, when information is scarce, to extend their recommendations beyond rigorously tested hypotheses and into professional judgment as a means of minimizing risk to the species.”17 The NRC Panel members also noted that the charge to their committee required them to use a different burden of proof than would be applicable under the ESA.18

Jeff Mount, a NRC committee member and UC Davis geologist, stated in regards to the NRC committee's charge that "The genius of the Klamath thing was the way they asked the questions.  Someone who is clever can design the questions in a way they can get the answer they're looking for, or that they're hoping for." Mount went on to state, "I hate it that I feel like we were manipulated for political reasons.”19

Interference and Consequences

This high-level pressure eventually came to bear on the rank-and-file NMFS scientists charged with undertaking the biological assessments. The 2002 NRC interim report cleared the way for water to be released to the farmers, but first the 2001 NMFS BiOp needed to be revised.

NMFS biologist Michael Kelly was designated as the technical lead for the NMFS team in charge of drafting the 2002 biological opinion, but later he would request to be dismissed from the project because of political pressure to adopt a specific plan that he felt was not biologically sound. Kelly relates that his team was denied “the opportunity to conduct obviously necessary analyses” and was pressured to adopt a specific interpretation of the results of the interim NRC report.20 He described the pressure as akin to being asked to “support the conclusion that 1+1=3.”21

The NMFS team was placed under considerable pressure to sign off on an RPA proposed by BOR in late April 2002. Under the BOR plan, adequate water flows would not be provided by the Klamath Project for the first eight years of the ten year plan, and no analysis was conducted to explain why such a plan would not jeopardize the survival of the species during that time period.22

At a joint meeting, the NMFS biologists stated they needed time to understand the impact of BOR’s proposal. During that meeting Kelly stated that Jim Lecky, a NOAA Assistant Regional Administrator in charge of the NMFS team, was told by higher-ups in the Commerce Department to stop “stonewalling” the BOR proposal. Following a private discussion between Lecky and BOR officials, Lecky stated that the NMFS would accept the BOR’s proposal without further analysis. Kelly felt that it was “obvious that someone up the chain of command was applying a tremendous amount of pressure on Mr. Lecky.”23 Following the decision not analyze the probable impacts of the RPA, Kelly asked to be removed from the project.

On April 1, 2002, while the revised BiOp was still being negotiated, Interior Secretary Gale Norton and Senator Gordon Smith opened irrigation gates to mark the beginning of the irrigation season by diverting more water to the farmers.24 In September of that year, low water levels, together with other factors, contributed to a large fish kill that claimed the lives of more than 33,000 adult salmon, steelhead trout, and other fish species in the lower 36 miles of the Klamath River.25 A large majority of the dead fish were non-endangered Chinook salmon, but the U.S. Fish & Wildlife Service estimated that several dozen wild coho salmon were also killed – a large number for an endangered species.26

Later that year, after determining that the manipulated BiOp would not be corrected internally, Kelly went public with his experiences and filed for whistleblower protection.27

Recent Developments

In 2005, in response to a lawsuit by the Pacific Coast Federation of Fishermen’s Associations, a judge threw out the 2002 BiOp and concluded that BOR and NMFS had failed to adequately analyze the impact of the first phases of the ten year plan to determine if the policy would jeopardize the coho salmon.28 In response to Congressional amendments,29 a recovery plan for the Klamath River coho salmon was released in July 2007.30 The Department of Commerce’s Inspector General, John M. Seeba, testified before the House Natural Resources Committee that department officials bypassed the standard procedures by not involving the NMFS regional Section 7 coordinator in creating or reviewing the 2002 BiOp.31

On May 14, 2004, Mike Kelly resigned from the National Marine Fisheries Service. Faced with yet another instance where a biological opinion that he was authoring would likely be politicized and overruled by superiors, he was compelled to leave his job as a fishery biologist. In his resignation letter Kelly stated, “I speak for many of my fellow biologists who are embarrassed and disgusted by the agency's apparent misuse of science.”32

1. U.S. Fish and Wildlife Service. Regulatory profile: Lost River sucker.
2. U.S. Fish and Wildlife Service. Regulatory profile: shortnose sucker.

3. U.S. Fish and Wildlife Service. Regulatory profile: coho salmon. Note: the sub-population in question is the Southern Oregon/Northern California Coast (SONCC) coho salmon.

4. U.S. Bureau of Reclamation (BOR). Klamath Project: California and Oregon.
Brazil, E. 2001. Farmers protest loss of water; 10,000 protest water cutoffs. San Francisco Chronicle, May 8. BOR Klamath Project.
6. U.S. Fish and Wildlife Service. Consultations with Federal Agencies.
7. NMFS is a part of the National Oceanic and Atmospheric Administration (NOAA, a part of the Department of Commerce) and is also known as the NOAA Fisheries.
8. National Marine Fisheries Service (NMFS). 2001. Biological Opinion: Ongoing Klamath Project Operations. April 6.

9. See for example, periodic drought maps from the Drought Monitor Archive.

10. Brazil. 2001.
11. Becker, J. and Gellman, B. 2007. Leaving No Tracks. Washington Post, June 27.
12. Ibid.

13. Hamburger, T. 2003. Oregon Water Saga Illuminates Rove's Methods With Agencies. Wall Street Journal. July 30.

14. Becker and Gellman 2007.
15. National Research Council (NRC). 2002. Scientific Evaluation of Biological Opinions on Endangered and Threatened Fishes in the Klamath River Basin: Interim Report. Washington, DC: National Academy Press.
16. Cooperman, M.S. and  Markle, D.F. “The Endangered Species Act and the National Research Council’s interim judgment in the Klamath Basin,” Fisheries, March 2003, vol. 28, no. 3.
17. National Research Council (NRC). 2004. Endangered and Threatened Fishes in the Klamath River Basin: Causes of Decline and Strategies for Recovery. Washington, DC: National Academy Press.
18. NRC 2004, p. 314.
19. Taugher, M. 2009. “Farm baron gets high-level help.” Contra Costa times, September 19.
20. Kelly, M. 2002, Narrative Statement of Michael S. Kelly, fishery biologist, National Marine Fisheries Service. Included in documents filed with the U.S. Office of Special Counsel.
21. Kelly, M. 2007. Testimony before the House Natural Resources Committee, July 31.
22. Kelly narrative. 2002.
23. Kelly testimony. 2007.
24. Hamburger. 2003.
25. Lynch, D.D. and Risley, J. C. 2003. Klamath River Basin hydrologic Conditions Prior to the September 2002 Die-Off of Salmon and Steelhead: U.S. Geological Survey-Resources Investigations Reports 03-4099; California Department of Fish and Game, 2004. September 2002 Klamath River Fish-Kill: Final Analysis of Contributing Factors and Impacts.
26. U.S. FWS. 2003. Klamath River Fish Die-Off September 2002: Report on Estimate of Mortality. November 7.
27. Kelly testimony. 2007.
28. Pacific Coast Federation of Fishermen’s Association v. Bureau of Reclamation, 138 F. Supp.2d 1228 (D. N.D. Cal. 2001).
29. U.S. Department of Commerce. Magnuson-Stevens Fishery Conservation and Management Act. May 2007.
30. National Marine Fisheries Service. 2007. Magnuson-Stevens Reauthorization Act: Klamath River Salmon Recovery Plan. July 10.
31. Office of the Inspector General. 2005. The NMFS Review Process for the California Central Valley and State Water Projects’ Biological Opinion Deviated from the Region’s Normal Practice.  Final Audit Report No. STL—17242-5-0001.  U.S. Department of Commerce, p. 14.
32. Kelly, M. 2004. Letter to NOAA and NOAA Fisheries Leadership, Re: My Resignation. May 18.

Powered by Convio
nonprofit software