Biological Opinions - Bureau of Reclamation

In 2001, the Services issued BiOps on the effects of Reclamation’s Project operations on listed
species, and concluded that the proposed Project operations would likely jeopardize the
continued existence of the Lost River sucker (LRS) and the shortnose sucker (SNS) in UKL
(USFWS 2001) and the Southern Oregon/Northern California Coast (SONCC) coho salmon
Evolutionarily Significant Unit (ESU) (NMFS 2001a). Because of a severe drought in 2001 and
the jeopardy BiOps, Reclamation limited the volume of water delivered to Project agricultural
users, and to the Lower Klamath and Tule Lake National Wildlife Refuges.
In early 2002, the National Research Council (NRC) concluded that “all components of the BiOp
issued by the USFWS on the endangered suckers have substantial scientific support except for
the recommendations concerning minimum water levels for Upper Klamath Lake.” The NRC
(2002a) “found a sound scientific basis for recommendations in the NMFS 2001 BiOp involving
coordination of operations and reduction of ramping rates for flows below the mainstem dams.”
However, the NRC found little scientific support for minimum mainstem flows to maintain and
recover coho salmon populations. Nevertheless, the NRC did not conclude that NMFS must be
wrong in its recommendations on mainstem flows that were included in the NMFS 2001 BiOp as
a reasonable and prudent alternative (RPA; NRC 2002b). The NRC (2002a, 2004) also noted
that Reclamation’s proposed lake and river flows, which would have caused lower mean lake
levels or lower minimum river flows, lacked scientific justification.
In March 2002, one month after the NRC issued its Interim Report (NRC 2002a), Reclamation
finalized a new BA that covered Project operations from May 31, 2002, to March 31, 2012, and
requested consultation with the NMFS and the USFWS. The USFWS issued a BiOp (finalized
in May 2002) that Reclamation’s implementation of this new proposal was likely to jeopardize
the continued existence of the LRS and the SNS, and provided an RPA that involved application
of an adaptive management approach that still allowed for Project water deliveries. NMFS
finalized a BiOp on May 31, 2002, and concluded that Reclamation’s proposed operations would
likely jeopardize the continued existence of the SONCC coho salmon and would likely adversely
modify critical habitat of SONCC coho salmon. In coordination with Reclamation, the NMFS’
BiOp also included a RPA that consisted of Reclamation operating the Project to ensure that IGD
minimum flows increased gradually over three phases during the 10-year period of the plan for
Project operations, among other additional requirements. Reclamation provided full water
deliveries to irrigators in 2002 despite the continued drought.
In September 2002, at least 33,000 adult salmonids died in the lowermost 40 miles of the
mainstem Klamath River (CDFG 2004a, Guillen 2003, NRC 2004, Yurok Tribal Fisheries Program
2004). The fish kill was unprecedented and affected primarily Chinook salmon, although coho
salmon (approximately 344), steelhead, and green sturgeon also died. The immediate cause of
mortality was massive infections of Ichthyopthirius multifilis (ich) and the bacterial pathogen
Flavobacter columnare (columnaris; CDFG 2003, Guillen 2004a, NRC 2004, Yurok Tribal Fisheries
Program 2004).
Several fisheries groups, environmental organizations, and tribes filed suit against Reclamation
and the NMFS in Federal district court, alleging violations of the ESA. The district court
overturned a significant aspect of the RPA, finding the requirement that Reclamation provide
only 57 percent of the long-term flows to be arbitrary and capricious. The issue on appeal was
the district court’s determination that Phases I and II of the RPA, or the short term measures,
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