Biological Opinions - Bureau of Reclamation

salmon under the proposed action. While NMFS cannot quantify the magnitude of the increased
disease risk to coho salmon under the proposed action, based on the reasons discussed above,
NMFS concludes that the proposed action will result in disease risks to coho salmon that are
lower than under observed POR conditions yet higher than under natural flow conditions.
12.4.1.2.3.4 Flow Variability
As discussed in the Hydrologic Effects section (i.e., section 11.4.1.1.3), the proposed action will
result in a mainstem Klamath River hydrograph that approximates the natural flow variability of
the upper Klamath Basin. Under the proposed action, the extent of the flow variability in the
mainstem Klamath River will be representative of natural hydrologic conditions in the upper
Klamath Basin (e.g., mainstem flows will increase when snow melt, precipitation, or both
increases in the upper Klamath Basin). For example, when the upper Klamath Basin is
experiencing relatively wet hydrologic conditions, flows in the mainstem Klamath River will be
relatively high seven days later. Conversely, when the upper Klamath Basin is experiencing
relatively dry hydrologic conditions, flows in the mainstem Klamath River will be relatively low
seven days later. The effects of the proposed action on flow variability will be greatest proximal
to IGD and diminish longitudinally, as tributary accretions contribute to the volume of water and
impart additional flow variability.
Flow variability is an important component of river ecosystems which can promote the overall
health and vitality of both rivers and the aquatic organisms that inhabit them (Poff et al 1997,
Puckridge et al. 1998, Bunn and Arthington 2002, Arthington et al. 2006). Arthington et al.
(2006) stated that simplistic, static, environmental flow rules are misguided and will ultimately
contribute to further degradation of river ecosystems. Variable flows trigger longitudinal
dispersal of migratory aquatic organisms and other large flow events allow access to otherwise
disconnected floodplain habitats (Bunn and Arthington 2002), which can increase the growth and
survival of salmon fry (Jeffres et al. 2008).
The proposed action will result in more natural and variable fall and spring flows that better
represent climate conditions, and will provide transitory habitat in side-channels and margins
preferred by coho salmon fry when flows increase in the spring. Transitory habitat in side
channels and margins is expected to provide suitable cover from predators, and ideal feeding
locations.
Variable flows, including small variations, provide dynamic fluvial environments in the
mainstem Klamath River that may impair polychaete fitness, reproductive success, or infection
with C. shasta. Since polychaetes appear to prefer stable hydrographs (Strange 2010b, Jordan
2012), flow variability will likely decrease polychaete habitat. In addition, polychaetes must
extract C. shasta myxospores from the water to become infected (Jordan 2012). Increased flow
variability may increase water velocity where polychaetes may have increased difficulty extracting
myxospores or colonizing habitat. If sufficiently large, increased flow variability under the
proposed action will likely help disrupt the fine sediment habitat of M. speciosa and increase the
redistribution of adult salmon carcasses in the mainstem Klamath River, which will likely reduce
polychaetes in the mainstem Klamath River. In addition, when the upper Klamath Basin is
experiencing relatively wet hydrologic conditions in the spring, flow variability under the
proposed action will result in a relatively smaller reduction to mainstem flows during the spring,
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