Biological Opinions - Bureau of Reclamation

in some tributaries, access to and from these areas is hindered by dams and diversions, the
existence of alluvial sills, and the formation of thermal barriers at the confluence of tributaries
and stagnant, disconnected pools. Where low flows have not restricted juvenile movements,
there are thermal refugial pools and tributaries available where water temperatures are suitable
for growth and survival, providing a limited amount of rearing habitat in the basin. Therefore,
the conservation value of the juvenile migration corridor is not properly functioning in the Scott
River. In dry water years, the Scott River Water Trust has obtained water leases to improve
migration flows for adult salmon during the fall, which has improved the migration corridor for
coho salmon in recent years.
11.3.5.3 Adult Migration Corridor
The current physical and hydrologic conditions of the adult migration corridor in the Scott River
reach are likely properly functioning in a manner that supports its conservation role of the adult
migration corridor. Water quality is suitable for upstream adult migration, and flow volume is
above the threshold at which physical barriers are likely to form.
11.3.5.4 Spawning Areas
Spawning activity and redds have been observed in the East Fork Scott River, South Fork Scott
River, Sugar, French, Miners, Etna, Kidder, Patterson, Shackleford, Mill, Canyon, Kelsey,
Tompkins, and Scott Bar Mill Creeks. Other than the two anthropogenic barriers on Etna Creek
and the mainstem Scott River, gravel transport in the Scott River Valley basin is unimpeded.
Pebble count data and survey data indicate that suitable gravels sizes are found in conjunction
with slopes also suitable for spawning (Cramer Fish Sciences 2010). These observations suggest
that the amount of coarse sediment and its rate of delivery are not limiting spawning habitat
availability in the Scott River Watershed.
Although gravel mobilization is unimpeded, historic land uses create a legacy of effects that are
continuing to impact available spawning habitat. Data shows that spawning substrate is largely
suitable throughout the basin, but the spatial extent of these areas is limited due to mine tailing
piles and other legacy mining effects. Current conditions in the Scott River mimic hydraulic
conditions similar to bedrock canyons where sediment used by salmonids has a lower likelihood
of persistence due to increased (or more efficient) sediment transport compared to unconfined
reaches (Cramer Fish Sciences 2010). The over extraction of streambed alluvium likely also
have stripped the alluvial cover from some river reaches exposing underlying bedrock, the net
result of which is enhanced sediment transport, less persistent alluvium, and an overall loss of
physical complexity (Cramer Fish Sciences 2010). Channel confinement by historic mining
tailings indirectly affects the diversity of stream habitat that might otherwise be available. Many
of these tailing piles are too large for the adjacent watercourse to reshape.
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