Biological Opinions - Bureau of Reclamation

Sutton and Soto (2010) documented several Klamath River tributaries (i.e., Cade [RM 110] and
Sandy Bar [RM 76.8] creeks) where fish access into the creeks was challenging, if not
impossible, when IGD flows were 1000 cfs in the summer. Because of their alluvial steepness,
NMFS acknowledges that some tributaries (e.g., Sandy Bar Creek) may not be conducive to
access until flows are very high, which may not be possible in the summer even without the
proposed action. Stage height-flow relationship data at mainstem Klamath River gage sites (e.g.,
Seiad or Orleans), indicate that during low summer flow conditions, 100 cfs influences the
Klamath River stage height by 0.1 to 0.13 feet. Given the minimal effect on stage height,
combined with overriding factors influencing passage from the mainstem into tributaries (e.g.,
tributary gradient and flow), NMFS does not anticipate the proposed action will have an adverse
effect on coho salmon juvenile migration corridors into tributaries.
11.4.1.2.3 Rearing Habitat
Rearing areas provide essential features such as cover, shelter, water quantity, and space. The
following discussion on the effects of the proposed action on rearing habitat is best categorized
by the affected essential features of critical habitat, which include cover, shelter, space, and
water quality. Cover, shelter, and space are analyzed together as habitat availability. Specific
areas of rearing habitat most influenced by flow include side channels and floodplain access,
which have greater opportunity to become inundated under a natural hydrology. NMFS also
evaluates the efficacy of channel maintenance flows on coho salmon critical habitat.
11.4.1.2.3.1 Coho Salmon Fry
As discussed in the Environmental Baseline section, coho salmon fry are present in the mainstem
Klamath River from March to approximately mid-June (Justice 2007). Therefore, effects to coho
salmon fry habitat are only addressed for the March through mid-June period. The proposed
action reduces flow volume in the mainstem Klamath River generally throughout most of the
year. Therefore, NMFS assumes that in locations where there are positive relationships between
flow and habitat, the proposed action reduces habitat availability (Figure 11.17). While NMFS’
ability to quantify proposed action effects are confounded, NMFS expects the range of proposed
action effects resulting from flow reductions on mainstem Klamath River coho salmon fry
habitat availability will vary considerably, from having no effect to levels that NMFS considers
adverse.
Between IGD and the Shasta River (RM 176), habitat for coho salmon fry increases as flows
increase from 1000 cfs to 4,100 cfs. However, for the purpose of analyzing effects of the
proposed action on coho salmon and their critical habitat, NMFS focused its analysis on those
conditions when habitat availability is less than 80 percent of maximum available. As described
in the Flow and Rearing Habitat Analysis section (i.e., section 11.1.3), when habitat availability
is at least 80 percent of maximum, the proposed action is not expected to adversely affect the
function of essential features of coho salmon critical habitat. The proposed action generally
lowers flows, and therefore habitat is generally reduced from IGD to the Shasta River when
flows range from 1000 cfs to 2,350 cfs (Figure 11.17). Using the same logic for the downstream
reaches, NMFS assumes that when the proposed action contributes to mainstem flows of
approximately 1,000 to 3000 cfs at the mouth of the Shasta River (RM 176), coho salmon fry
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