Biological Opinions - Bureau of Reclamation

7.11.1 Clear Lake
The major known threats to LRS and SNS in Clear Lake are prolonged drought and bird
predation. Entrainment might also be a threat, but has not been studied. Water quality and
disease are not normally issues at Clear Lake but, during droughts and periods with low lake
levels, parasitism and food abundance might be factors adversely affecting suckers. The effects
of drought on suckers in Clear Lake were covered in previous consultations, the most recent
being the USFWS 2008 BO and Reclamation’s 2012 BA, which has a lengthy description of
Clear Lake hydrology and the effects of drought. Because there are several recent hydrologic
baseline analyses for Clear Lake, we will focus only on the main points here (USFWS 2002,
2008, Sutton and Ferrari 2010).
Periodic low inflows into Clear Lake, combined with irrigation diversions, high seepage, and
evaporative losses, can result in low water levels during multiyear droughts, as experienced in
2009–2010. During drought conditions the lake level continues to decline as a result of
evaporation and seepage, even without irrigation releases. This is because annual April through
October evaporative and seepage losses from Clear Lake average approximately 44,000 acre-feet
while seasonal irrigation releases average about 38,000 acre-feet (Reclamation, unpublished
data).
Low lake levels can adversely affect LRS and SNS by limiting access to Willow Creek, the only
known spawning area for the suckers in Clear Lake (USFWS 2002, 2008). A minimum lake
level of about 4,524.00 ft (1,378.92 m) is believed necessary to provide spawning access to the
creek (Reclamation 2003, USFWS 2008). Impaired access to Willow Creek can prohibit or
reduce sucker reproduction at Clear Lake in any given year. A survey of hydrologic connectivity
of lower Willow Creek, the channel between the east lobe of Clear Lake and Clear Lake Dam,
and the channel between the east and west lobes of Clear Lake, indicated that a hydrologic
control point at an elevation of 4,521.70 ft (1,378.21 m) exists between the east lobe and the
mouth of Willow Creek (Sutton and Ferrari 2010). A functional disconnect occurs between
surface waters of the east lobe and the dam, including the mouth to Willow Creek, when the east
lobe of Clear Lake drops below an elevation of about 4,522.00 ft (1,378.31 m; Sutton and Ferrari
2010). At a lake elevation of 4,525.00 ft (1,379.22 m), this hydrologic control is inundated with
approximately 3 ft (less than 1 m) of water, which available information indicates is sufficient
for passage by adult suckers, but still so shallow that it could expose them to pelican predation.
Detections of passive integrated transponder (PIT)-tagged adult suckers in Willow Creek in
relation to lake elevations measured at the dam indicate that LRS and SNS movement into
Willow Creek from 2006 through 2011 appears to be predominantly a function of Willow Creek
discharge. Adult suckers appear to enter the creek on a cue of creek discharge, but lake elevation
may also play an important role in some years (Barry et al. 2009; USBR 2012). In years with
higher lake elevation relatively large numbers of tagged suckers were detected in spawning runs.
However, in years when there are no substantial inflows, spawning migrations are relatively
small in numbers regardless of lake elevations. The number (n = 121) of PIT-tagged adult
suckers detected in Willow Creek in 2007 was 7 and 9.5 times lower than in 2006 and 2008,
respectively (Barry et al. 2009). Water levels in Clear Lake on February 1, 2007 were relatively
high (4528.21 feet [1380.20 m]), but the flows through April 29 were very low, increasing the
overall water level by only 5 inches (12.5 cm), even though no withdrawals were occurring. In
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