population isolates. Most of the current WSCT work occurs in core area watersheds or 

 streams containing known fluvial WSCT (Pierce et al. 1997; 2001; 2002; 2004; Results 

 Part III) 



To date, restoration projects in WSCT habitat have involved 38 streams. Projects 

 focus on improving habitat conditions in both fluvial and resident isolet WSCT 

 populations. In 2004 and 2005, the Blackfoot Cooperators continued to develop or 

 implement projects on 13 WSCT-bearing streams (Arrastra Creek, Ashby Creek, 

 Clearwater River, Cottonwood Creek, Murphy Spring Creek, Nevada Creek, Nevada 

 Spring Creek, North Fork Blackfoot, Rock Creek, Pearson Creek, Poorman Creek, 

 Snowbank Creek and Wasson Creek), during which time FWP monitored WSCT 

 populations on 1 7 project streams (Results Part III). 



During 2004 and 2005, we expanded fisheries inventories to the backcountry of 

 the watershed, including both lakes and streams in wilderness and roadless areas. We 

 inventoried three streams in the headwaters of the North Fork and 13 mountain lakes of 

 the upper Landers Fork and North Fork drainages (Results Part IV). Initial 

 Oncorhynchus genetic testing indicates mild introgression in waters of the Dry Fork arm 

 of the North Fork. However, initial genetic testing of mountain lakes in upper Landers 

 Fork and East Fork of the North Fork basin reveal hybrid swarms of rainbow trout, 

 Yellowstone cutthroat trout and WSCT in certain headwater lakes (Results Part IV; 

 Appendix I). Additional backcountry inventories and genetic tests will continue through 

 2007. We also re-tested WSCT populations in two streams - Union and Game Creeks 

 and tested the North Fork of Frazier Creek (Appendix I). 



In response to harvest restrictions and tributary restoration, densities of fluvial 

 WSCT have been increasing in the lower Blackfoot River (Johnsrud and Scotty Brown 

 Bridge sections) since 1990 (Results Part II). In 2004, WSCT estimates (>6.0") ranged 

 from a low of -0.5 fish/1000' below Nevada Creek (Wales Creek Section) to 14-18 

 fish/1000' at monitoring stations of the lower river (Johnsrud and Scotty Brown Bridge 

 sections). Low densities in the Wales Creek section reflect impaired water quality and 

 degradation of nearby tributaries. In the Scotty Brown section, WSCT densities are 

 generally stable compared with other trout species - all of which have declined in this 

 section during the drought (Results Part II). 



The distribution of whirling disease is generally at elevations below most known 

 WSCT spawning and rearing sites with some exceptions, including Chamberlain Creek - 

 an important fluvial WSCT spawning stream in lower Blackfoot Watershed. Continued 

 monitoring of WSCT in Chamberlain Creek during 2004-05 suggests stable densities in 

 the presence of high infection levels (Results Part III). 



STUDY AREA 



The Blackfoot River is one of twelve renowned '"''Blue Ribbon " trout rivers in 

 Montana with a 1 972 appropriated ''Murphy" in-stream flow water right of 700 cfs at the 

 USGS Bormer (#12340000) gauging station. The Blackfoot River, located in west central 

 Montana, begins at the junction of Beartrap and Anaconda Creeks, and flows west 132 

 miles fi-om its headwaters near the Continental Divide to its confluence with the Clark 

 Fork River in Bonner, Montana (Figure 4). Mean annual discharge is 1 ,563 cubic-feet- 

 per-second (cfs) near the mouth (USGS 2005 provisional data). 



This river system drains a 2,320 square mile watershed through a 3,700-mile 



12 



