September 2003. Cottonwood Creek also supports a high-grade whirUng disease 

 infection in the lower stream reaches. The upper stream reaches have remained negative 

 for the presence of WD. Both reaches have been monitored between 1998 and 2003 

 (Results Part IV). 



Project Monitoring Density (95% CO 



In 2002 and 2003, we 

 continued to monitor fish 

 populations in upper Cottonwood 

 Creek in the area of a water lease, 

 downstream of the Dreyer 

 Diversion. The water lease was 

 initiated in 1997, prior to which 

 time a major diversion (Dreyer 

 Diversion) completely dewatered a 

 portion of Cottonwood Creek 

 during the late irrigation season. 



Fish population monitoring 

 in the water lease area (stream mile 

 12.1) show increasing densities of 

 WSCT following increased flows. The 2003 fish population data show densities of 

 WSCT (> 4.0") have declined since the 2001, likely the result of extended drought 

 (Figure 21). 



At stream mile 16, near the upper culvert problem, we recorded a CPUE for 

 WSCT of 2.4 fish/100' above the culvert compared with 4.6 below the culvert. All fish 

 captured below the culvert were concentrated near the culvert. We found very low 

 numbers of bull trout below the culvert (CPUE = 0.2) and no bull trout upstream of the 

 culvert. 



Figure 21. Estimated densities of WSCT (fish > 4.0") 

 in Cottonwood Creek at mile 12.1. 1996-2003. 



Chamberlain Creek 



Restoration objectives: improve access to spawning areas; improve rearing conditions for 

 WSCT; improve recruitment of WSCT to the river; provide thermal refuge and rearing 

 opportunities for fluvial bull trout. 



Project Summary 



Chamberlain Creek is a small Garnet Mountain tributary to the middle Blackfoot 

 River, entering at river mile 43.9 with a base flow of -2-3 cfs. Sections of lower 

 Chamberlain Creek were severely altered, leading to historic declines in WSCT densities. 

 Adverse changes to stream habitat included channelization, loss of instream wood, 

 dewatering, excessive riparian livestock access, road encroachment, and elevated 

 instream sediment from road drainage. Other problems included fish losses to irrigation 

 ditches, impaired fish passage, and more recently the escalation of whirling disease in 

 lower reaches. 



Since 1990, Chamberlain Creek has been the focus of a comprehensive fisheries 

 restoration effort. Projects include: road drainage repairs, riparian livestock management 



36 



