Biological Opinions - Bureau of Reclamation

conditions may fail if those conditions occur less frequently or intensely (as is predicted) or if
human activities degrade riverine habitats.
In the action area, all five populations in the Interior Klamath River stratum may be adversely
affected by the proposed action. NMFS believes that the populations within the Interior Klamath
River stratum have a moderate to high extinction risk. Abundance estimates indicate that all of
the populations within the stratum fall below the levels needed to achieve a low risk of
extinction. The large proportion of hatchery coho salmon to wild coho salmon reduces diversity
and productivity of the wild species. However, due to the low demographics of the Upper
Klamath and Shasta River populations, IGH coho salmon strays are currently an important
component of the adult returns for these populations because of their role in increasing the
likelihood that wild/natural coho salmon find a mate and successfully reproduce. Iron Gate and
Trinity River Hatchery Chinook salmon smolts compete with wild coho salmon for available
space and resources. Poor habitat and water quality conditions in the Shasta and Scott River
basins disperse larger numbers of coho salmon fry and parr out of the Shasta and Scott basins
and into the mainstem Klamath River each spring than would otherwise occur if these tributaries
met the ecological needs of coho salmon (Chesney and Yokel 2003). While not restricted to the
Shasta and Scott rivers, coho salmon fry and parr emigration in response to poor habitat
conditions appears to affect these two populations to a greater degree than other tributary-based
populations within the Klamath River Basin (NRC 2004).
In the Environmental Baseline section, NMFS described the current environmental conditions
that influence the survival and recovery of Klamath River coho salmon populations. Coho
salmon in the mainstem Klamath River will continue to be adversely affected by the ongoing
activities, such as agricultural diversions and PacifiCorp’s Klamath Hydroelectric Project,
although PacifiCorp’s Klamath Hydroelectric Project is expected to continue operating under an
incidental take permit and associated HCP during most of the term of the proposed action.
There has been a recent decline in UKL outflows since the 1960s, which is likely due to
increasing diversions, decreasing net inflows, or other factors (Mayer 2008). There have been
declines in winter precipitation in the upper Klamath Basin in recent decades and declines in
upper-Klamath Lake inflow and tributary inflow, particularly base flows (Mayer 2008).
Declines in tributary base flow could be due to increase consumptive use, in particular,
groundwater use, and/or climate changes. Agricultural diversions from the UKL have increased
over the 1961 to 2007 period, particularly during dry years (Mayer 2008). Declines in Link
River flows and Klamath River at Keno flows in the last 40-50 years have been most pronounced
during the base flow season (Mayer 2008), the time when agricultural demands are the greatest.
While the operation of the PacifiCorp’s dams will continue to block coho salmon access
upstream of IGD and degrade water quality, PacifiCorp’s HCP includes measures to minimize
and mitigate these effects to the maximum extent practicable. PacifiCorp, via the HCP,
committed to maintain and improve coho salmon spawning and rearing habitat in the Upper
Klamath River tributaries by: (1) maintaining and improving access to existing spawning and
rearing habitat in approximately 60 miles of Upper Klamath tributaries, and (2) removing
existing passage barriers to create permanent access to at least one mile of potential spawning
and rearing habitat in Upper Klamath tributaries. In addition, PacifiCorp will implement a
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