Biological Opinions - Bureau of Reclamation

limited empirical observations of coho salmon fry and parr in the mainstem Klamath River
(Hardy et al. 2006).
Using simulated hydrodynamic variables at intensive study sites, Hardy developed composite
suitability indices for each site from the habitat suitability criteria data, which incorporated
species and life-stage specific preferences with regard to specific microhabitat features, such as
flow, depth, velocity, substrate, and cover characteristics. The composite suitability indices were
later converted into a combined measure known as the weighted usable area (WUA) to
characterize the quality and quantity of habitat in terms of usable area per 1,000 linear feet of
stream (NRC 2008). Hardy et al. (2006) then scaled up WUA results from the individual sites to
the larger reach-level scale (see Hardy et al. 2006 or NRC 2008 for further discussion). WUA is
a measure of habitat suitability, predicting how likely a habitat patch is to be occupied or avoided
by a species life stage at a given time, place, and discharge (i.e., the suitability of the habitat for a
specific species and life-stage of fish; NRC 2008).
NMFS uses reach-level WUA curves to gauge the general change in instream habitat availability
(incorporating both quantity and quality) within the mainstem Klamath River resulting from the
proposed action, and characterizes the change as a difference in suitable habitat volume. NMFS
uses WUA curves from reach-level study sites for the Upper Klamath and Middle Klamath River
reach effects analyses (Table 11.1).
Table 11.1. Hardy et al. (2006) and Hardy (2012) reach-level study sites used by NMFS for analysis.
Klamath River Reach Coho Salmon Fry Coho Salmon Juvenile*
IGD to Shasta River
Trees of Heaven
Shasta to Scott rivers
Upper Klamath River Reach
Parts of Scott to
Seiad Valley
Salmon rivers
Middle Klamath River Reach Parts of Scott to
Rogers Creek
Salmon rivers
*While Hardy et al. (2006) developed WUA curves for coho salmon juveniles at
seven reaches in the Klamath River, NMFS uses only the Trees of Heaven, Seiad
Valley, and Rogers Creek reaches because these reaches have relatively high habitat
availability and are most influenced by the proposed action (i.e., closest to IGD).
Unlike the previous BiOp (NMFS 2010a), Reclamation did not model a No-Project flow
scenario. The No-Project hydrology was used to describe a reference condition of a hydrological
setting with all aspects of the baseline other than Reclamation’s discretionary actions, thereby
providing the Services with a reference condition to evaluate the effects of Reclamation’s
proposed action on UKL elevations and Klamath River flows below IGD. A No-Project flow
scenario for the Klamath River is dependent upon a number of critical assumptions (e.g.,
designating the UKL outflow elevation, Refuge deliveries, Lost River diversions to and from the
Klamath River, and other water routing assumptions that influence the magnitude, timing and
duration of flows in the Klamath River). While anthropogenic factors influencing water
availability and routing outside of Reclamation’s discretion remain in a No-Project flow
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