Biological Opinions - Bureau of Reclamation

habitat availability. In those flow ranges, when flows increase, habitat availability increases.
Conversely, when flows decrease, habitat availability decreases in those flow ranges. Therefore,
when the proposed action reduces mainstem flows within those ranges, the proposed action
reduces habitat availability.
Like the previous BiOp (NMFS 2010a), NMFS assumes at least 80 percent of maximum
available habitat provides for the conservation needs of coho salmon, and excludes flows that
provide at least 80 percent of maximum available habitat from the analysis. NMFS then
highlights the time periods and flow exceedances when the proposed action will reduce habitat
availability below 80 percent of maximum available habitat for each reach. Instream maximum
available habitat of 80 percent has been used to develop minimum flow needs for the
conservation of anadromous salmonids (Sale et al. 1981 in Clipperton et al. 2002, NMFS 2002,
Alberta Environment and Department of Fisheries and Oceans Canada 2007, Hetrick et al. 2009).
Therefore, NMFS assumes that at least 80 percent of maximum available habitat provides a wide
range of conditions and habitat abundance in which populations can grow and recover. Where
habitat availability is 80 percent or greater under the proposed action, habitat is not expected to
limit individual fitness or population productivity or distribution nor adversely affect the function
of essential features of coho salmon critical habitat.
NMFS is aware of the limitations of focusing solely on WUA analysis when analyzing an
individual coho salmon or coho population’s response to an action (e.g., NRC 2008). For
example, whether or not individuals actually occupy suitable habitat is dependent on a number of
factors that may preclude access, including connectivity to the location, competition with other
individuals, and risks due to predation (Hardy et al. 2006). Like all models, the instream flow
model developed by Hardy et al. (2006) is an imperfect representation of reality (NRC 2008),
and uncertainty exists in the model. Thus, NMFS’ analysis focuses on habitat availability, as
well as other important components of the flow regime, like water quality, channel function, and
hydrologic behavioral cues, and how they affect coho salmon individual fitness.
Hardy et al. (2006) discussed the concept of an ecological base flow for the Klamath River. The
ecological base flow (also called environmental flow) represents the minimum flow where any
further anthropogenic reductions would result in unacceptable levels of risk to the health of
aquatic ecosystem (Tharme 2003, Arthington et al. 2006, Hardy et al. 2006, Beca 2008, Ohlson
et al. 2010). Hardy et al. (2006) adopted an ecological base flow for the Klamath River that is
equivalent to the monthly 95 percent exceedance level of their instream flow recommendations.
With regard to Hardy et al.’s (2006) instream flow recommendations, including the ecological
base flow, for the mainstem Klamath River, NMFS notes the different objectives and standards
for analyses in Hardy et al. (2006) and this BiOp. Specifically, Hardy et al. (2006) used a multispecies
approach to develop flow recommendations for conserving the entire suite of
anadromous salmonids inhabiting the Klamath River Basin. In contrast, NMFS must focus its
jeopardy and critical habitat analyses upon the effects of the proposed action on listed species
(i.e., SONCC coho salmon) and critical habitat designated for listed species. Nevertheless,
Hardy et al.’s (2006) instream flow recommendations provide NMFS with a useful reference
when analyzing expected flows under the proposed action. Hardy et al.’s (2006) instream flow
recommendations were based on the natural flow paradigm that concludes effective instream
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