Biological Opinions - Bureau of Reclamation

characteristics of aquatic species, such as coho salmon, the large size and variability of the
Klamath River, and the operational complexities of managing Klamath River flows, quantifying
individuals that may be taken incidental to the many components of the proposed action is
generally not possible. In addition, incidental take of coho salmon from the increased disease
risk is difficult to estimate because of the limited data on coho salmon-specific infection and
mortality rates. When NMFS cannot quantify the level of incidental take, NMFS uses surrogates
to estimate the amount or extent of incidental take.
For estimating incidental take from habitat reductions, elevated water temperatures, reductions to
dissolved oxygen concentrations, decreased smolt outmigration rates, and increased disease
risks, NMFS uses a hydrologic-based surrogate because water availability in the mainstem
Klamath River in the spring and summer has a direct effect on these sources of incidental take.
NMFS made a number of assumptions regarding water availability under the Proposed Action
that are within and outside the discretion of Reclamation’s actions. As a result of Reclamation’s
model output from the Proposed Action’s formulaic approach, NMFS made assumptions
regarding the shape of the annual hydrographs and then analyzed the effects of Reclamation’s
proposed action on coho salmon based on these assumptions. Included in those assumptions
outside of Reclamation’s discretion is the assumption that accretion timing, magnitude and
volume from Keno Dam to IGD in the proposed action period will be consistent with the
accretion timing, magnitude and volume modeled for the 1981-2011 period.
As discussed in the BiOp, NMFS identified that the proposed action will result in the incidental
take of coho salmon in the mainstem Klamath River due to habitat reductions during March
through June, elevated water temperatures during May to June, reductions to dissolved oxygen
concentrations during June to August, decreased smolt outmigration during April to June, and
increased disease risks during April to August. Since habitat reductions, elevated water
temperatures, reductions to dissolved oxygen concentrations, decreased smolt outmigration rates,
and increased disease risks are inextricably linked to flow, NMFS uses the minimum average
daily flows at IGD during March to August (Table 13.4) and the calculated EWA volumes
relative to the UKL Supply (Table 13.5) to measure the level of incidental take because the
minimum average daily IGD flows and the annual EWA volumes are within Reclamation’s
discretion.
NMFS cannot predict a specific proportion of the EWA distribution that will be incrementally
released during the March through August period, when NMFS anticipates incidental take of
coho salmon juveniles will occur, for a number of reasons. Distribution of the EWA during the
period March through September is dependent upon Williamson River flow as a hydrological
indicator to determine the releases from UKL at Link River Dam. In addition, releases at Link
River Dam during March through September also take into account accretions between Link
River Dam and IGD, UKL fill rate, water released for flood prevention, the volume of EWA that
needs to be reserved for the base flow period (June through September), and the volume of EWA
already used. During the July through September period, EWA releases may be reduced if IGD
maximum flow targets are anticipated to be exceeded, which results in surplus EWA stored for
release in October and November. This approach produces a hydrograph that reflects real-time
hydrologic conditions, while also requiring specific portions of the total EWA to be reserved for
use by specific dates. Nevertheless, NMFS expects the total EWA volume relative to the UKL
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