Biological Opinions - Bureau of Reclamation

While there will be reductions in rearing habitat availability, the proposed action does provide
flow variability in the mainstem Klamath River. Flow variability will occur during precipitation
and snowmelt events, reflecting qualities of a natural flow regime. When hydrologic conditions
in the upper Klamath Basin are wet, flow variability under the proposed action will result in
higher flows in the mainstem Klamath River downstream of IGD. Temporary increases in
mainstem flows are expected to result in short-term increases in the amount and quality of
habitat in the mainstem for fry and juvenile coho salmon. Therefore, the adverse effects to coho
salmon fry habitat in the mainstem Klamath River between IGD and the Salmon River are likely
to be somewhat moderated by the flow variability under the proposed action when hydrological
conditions in the upper Klamath Basin are wet. During dry hydrologic conditions in the Klamath
Basin, the proposed action will minimize adverse effects to coho salmon fry in April to June by
not reducing flows in the mainstem Klamath River below what Hardy et al. (2006) considers to
be acceptable levels of risk to the health of aquatic resources.
NMFS anticipates adverse effects to critical habitat from habitat restoration to be minor and
short-term as most restoration projects are anticipated to occur as one time disturbance events
within the summer period when flows are lowest. Short-term adverse effects to rearing habitat
will primarily occur as a result of dewatering the channel and increasing sediment input during
instream activities. Temporary reduction of rearing habitat can occur through dewatering habitat
and the filling of pools with fine sediment.
Despite the minor and short-term adverse effects, NMFS expects the suite of restoration
activities will result in long term improvements to the function and role of rearing habitat in the
action area. Approximately 71 percent of the four to six restoration projects implemented each
year will be successful at increasing the conservation value of coho salmon rearing habitat. For
example, instream habitat structures and improvement projects will provide cover for juveniles
to escape predators and rest, improve pool to riffle ratios, and add habitat complexity and
diversity. Stream bank stabilization projects will reduce sedimentation from watershed and bank
erosion, decrease turbidity levels, and improve water quality for coho salmon over the long-term.
In summary, the proposed action will likely reduce the quantity of coho salmon rearing habitat in
the mainstem Klamath River between IGD and the Salmon River, especially in the spring and
during below average water years. However, the proposed action is likely to increase the quality
of rearing habitat in the action area.
11.6.3.3.1.2 Water Quality
The proposed action is likely to increase water temperature in the mainstem Klamath River
between IGD and the Scott River by up to approximately 0.5 °C during the spring (Perry et al.
2011). Below the Scott River mouth, the proposed action’s effects on water temperature in the
spring are likely insignificant because cold water accretions and meteorological conditions have
a pronounced effect on water temperatures in the mainstem Klamath River. In the summer and
early fall, any decreases in IGD flows are likely to reduce water temperature in the mainstem
Klamath River because reservoir water behind IGD is warmer than the mainstem Klamath River.
In addition, the proposed action will likely contribute to adverse effects to the rearing habitat
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