Biological Opinions - Bureau of Reclamation

winter rearing habitat in the Scott River basin, limiting juvenile survival. Although rearing
habitat still exists in some tributaries, access to some of these areas is hindered by dams and
diversions, the existence of alluvial sills, and the formation of thermal barriers at the confluence
of tributaries. Where passage is possible, there are thermal refugial pools and tributaries where
the water temperature is several degrees cooler than the surrounding temperature, providing a
limited amount of rearing habitat in the basin.
Currently, valley-wide agricultural water withdrawals and diversions, groundwater extraction,
and drought have all combined to cause premature surface flow disconnection along the
mainstem Scott River. In addition, summer discharge has continued to decrease significantly
over time, further exacerbating detrimental effects on coho salmon in the basin. These
conditions restrict or exclude available rearing habitat, elevate water temperature, decrease
fitness and survival of over-summering juveniles, and sometimes result in juvenile fish
strandings and death. The conservation value of juvenile rearing areas is not properly
functioning in the Scott River.
Since 2007, the Scott River Water Trust has leased water from willing water right holders along
tributaries that drain the west side of the valley during the late summer months when many of
these tributaries have very little surface flow. These water leases allow the tributaries to remain
connected and have improved conditions for juvenile rearing during the summer.
Woody debris is scarce throughout the mainstem Scott River and its tributaries. Mainstem
habitat has been straightened, leveed, and armored. Anthropogenic impacts have resulted in a
lack of channel complexity from channel straightening and reduced amounts of woody material
(Cramer Fish Sciences 2010). The present-day mainstem Scott River bears minor resemblance
to its more complex historic form although meandering channel planforms are still present
(Cramer Fish Sciences 2010). The cumulative effect of these changes cannot be quantified.
However, both the amount and quality of habitat has been clearly reduced. Large woody debris
that is available along the mainstem corridor is highly mobile during high flow events, further
decreasing retention of large woody that does get recruited. Recent data regarding large woody
debris in tributaries indicates that recruitment is improving in the uplands, providing more
complex habitat and potential rearing areas in stream reaches above the valley.
11.3.5.2 Juvenile Migration Corridor
Physical fish barriers exist in the Scott River watershed. For instance, Big Mill Creek, a
tributary to the East Fork Scott River, has a complete fish passage barrier caused by down
cutting at a road culvert outfall (CalFish 2011). For many years, the City of Etna’s municipal
water diversion dam on Etna Creek effectively blocked fish passage into upper Etna Creek,
however this dam was retrofitted with a volitional fishway in 2010.
In addition, valley-wide agricultural water withdrawals and diversions, groundwater extraction,
and natural cycles of drought have all combined to cause premature surface flow disconnection
along the mainstem Scott River. These conditions can consistently result in restrictions or
exclusions to suitable rearing habitat, contribute to elevated water temperatures, and contribute to
conditions which cause juvenile fish stranding and mortality. Although rearing habitat still exists
225