Biological Opinions - Bureau of Reclamation

etween Trees of Heaven (RM 172) and Seiad Valley (RM 129) in May and June (Foott et al.
2008, Hallett et al. 2012, Ray et al. 2012). In addition, the proposed action will also likely
increase the percentage of coho salmon juveniles in the mainstem Klamath River between
Klamathon Bridge (RM 184) and Orleans (RM 59) that will experience sublethal effects of C.
shasta infections during April to August (Foott et al. 2008, Hallett et al. 2012).
12.4.1.2.4.3 Thermal refugia
Thermal refugia along the mainstem provide salmon essential locations where coho salmon
juveniles can seek refuge when water temperatures in the mainstem become excessive (Tanaka
2007). Without thermal refugia, mainstem flows alone could not support salmonid populations
in the summer because of the high water temperatures in the mainstem Klamath River (Sutton et
al. 2007). Coho salmon juveniles use refugial habitat in both the mainstem Klamath River and
non-natal tributaries as refuge from critically high mainstem Klamath River water temperatures
in the summer (Sutton et al. 2007, Soto et al. 2008, Sutton and Soto 2010). Sutton and Soto
(2010) found that coho salmon juveniles began using thermal refugia when the mainstem
Klamath River temperature approached approximately 19 °C. Similarly, Hillemeier et al. (2009)
found that coho salmon started entering Cade Creek, a cooler tributary, when mainstem Klamath
River temperature exceeded about 19 °C.
When coho salmon juveniles in the mainstem cannot access cooler tributaries, they can face
elevated stress from mainstem temperatures, degraded water quality, competition with other
salmonids for mainstem thermal refugia, and higher susceptibility to pathogens such as C.
shasta. Mainstem thermal refugia provide coho salmon relief from temperature and poor water
quality (e.g., high pH and low dissolved oxygen concentrations). However, mainstem thermal
refugia do not provide coho salmon relief from susceptibility to C. shasta if actinospore densities
are high (Ray et al. 2012).
The primary factor affecting the integrity of thermal refugia is the tributary flows, which are not
affected by the proposed action. The higher the tributary flows, the larger the thermal refugia
will be in the mainstem Klamath River. Tributaries that historically provided cold water
accretions to the mainstem Klamath River produce appreciably less water to the mainstem
Klamath River due to water diversions, provide less non-natal rearing habitat (e.g., Shasta and
Scott River), and reduce the amount of available thermal refugia in the mainstem.
While the proposed action does not affect the amount or timing of tributary flows, the proposed
action can influence both the size of refugial habitat in the mainstem Klamath River as well as
influence the connectivity between tributaries and the mainstem. When the proposed action
decreases mainstem flows in the summer, water temperature becomes more influenced by
meteorological conditions, which will increase daily maximum and median (to a lesser extent)
water temperatures. Elevated water temperatures in the summer may temporarily reduce the size
of thermal refugia in the mainstem (Ring and Watson 1999, Ficke et al. 2007, Hamilton et al
2011). On the other hand, the NRC (2002 and 2004) hypothesized that increasing mainstem
flows in the Klamath River might reduce the size of thermal refugia because of the warm water
temperatures out of IGD.
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