Biological Opinions - Bureau of Reclamation

decreased, culminating with a low of 32 percent in sampled fish at the Shasta to Scott River
reach by June 15 when IGD flows were approximately 1,200 cfs (Nichols et al. 2007).
In a laboratory setting, Foott et al. (2007) exposed IGH Chinook salmon juveniles to Klamath
River water in the spring of 2005 and found that C. shasta infections in Chinook salmon did not
decline between April and June despite the high flows in May of 2005. Foott et al. (2007) then
suggested that increasing spring flows is not effective at reducing parasite infection rates. NMFS
notes that the laboratory data using Klamath River water (Foott et al. 2007) is not as ideal as data
directly from fish sampled in the Klamath River. In addition, fish in the lab with Klamath River
water were confined to a small area where fish cannot easily avoid actinospores (i.e., tanks were
up to 15 liters [4 gallons]; Foott et al. 2007). Therefore, NMFS relies again on data from the
Klamath River (Nichols et al. 2007) to assess the proposed action’s effects on disease
prevalence.
High winter and spring flows in 2006 when IGD flows exceeded 10,000 cfs resulted in a general
reduction in seasonal disease rates and a delay in the peak infection rates among juvenile
salmonids in the mainstem Klamath River. Flows at IGD in the spring of 2006 may have
influenced disease infection rates by: (1) reducing the abundance of polychaete colonies due to
the scouring of slack water habitats and Cladophora beds, (2) diluting C. shasta actinospore
concentrations; and/or (3) reducing the transmission/infection efficiency of the parasites due to
environmental conditions (temperature, turbidity, velocity).
As discussed in the Hydrologic Effects section (i.e., section 11.4.1.1.4), the proposed action will
increase the magnitude and frequency of channel maintenance flows between 5,000 and 10,000
cfs relative to the observed POR (e.g., the proposed action will have an estimated two year flood
frequency of 5,454 cfs whereas the observed POR had 5,168 cfs). When compared to the
observed POR, the increase in magnitude and frequency of channel maintenance flows between
5,000 and 10,000 cfs under the proposed action will likely decrease the abundance of
polychaetes in the spring and summer following a channel maintenance flow event. In addition,
the increase in magnitude and frequency of channel maintenance flows between 5,000 and
10,000 cfs under the proposed action will likely decrease the actinospore concentrations relative
to the observed POR when the channel maintenance flow event occurs in the spring, particularly
in May and June.
However, the proposed action will decrease the duration of channel maintenance flows between
5,000 and 10,000 cfs relative to the observed POR (e.g., an average reduction of 7 days per year
with flows between 5,000 and 10,000 cfs), which will reduce the actinospore dilution effect of
high flows since the channel maintenance flows generally occur in the spring. Fewer days of
channel maintenance flows mean fewer days of actinospore dilution, which will likely increase
the density of actinospores in the May through June weeks following the high flow event.
The proposed action’s net disease effect to coho salmon from these varying hydrologic changes
to channel maintenance flows between 5,000 and 10,000 cfs is unclear, but is likely to be
improved over the observed POR because the increased magnitude and frequency of high flows
will provide more intense and frequent disturbance to polychaetes and sediment. Meanwhile,
the shorter duration of high flows may not necessarily decrease the relative effectiveness of
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