Cottonwood Creek, a third-order tributary, flows 16 miles south through a confined, high-gradient, and well-armored channel before entering the Blackfoot River at river mile 43. As the stream exits its canyon, sinuosity increases and a pool-riffle sequence develops. As the stream enters an outwash plain it loses water; an intermittent section occurs between stream mile 9 and 11, near the mountain-valley interface. The lack of water in this section is exacerbated by irrigation withdraws. In order to prioritize restoration resources, we developed a fisheries-based restoration priority scorecard, based on biological, social and financial considerations, for 83 impaired tributaries of the Blackfoot River. Cottonwood Creek ranked 5 of 83 streams surveyed.

Cottonwood Creek gains groundwater beginning at stream mile 9.0, and appears to be a gaining stream to the mouth due largely to three spring creeks located between river mile 6.3 and 7.5. Beaver activity greatly influence channel characteristics through most of this reach.

Two major irrigation diversions occur at stream miles 5 and 12. Below the upper diversion, the stream dries in low flow years for 2.5 miles. Management of the headgate has isolated westslope cutthroat trout and bull trout attempting to escape the dewatered section, resulting in fish kills. Additionally, both diversion structures were barriers to upstream movement of fish and entrained out-migrants. The upper diversion serves an 8,000 foot irrigation canal that irrigates approx. 400 acres of hay land. This canal was inefficient, carrying only 28% of its volume to the end-point.   At the time this information was recorded, the canal took the entire stream flow (8 cfs) to an irrigation pump with a 1 cfs capacity. Restoration projects in the Cottonwood Creek drainage began in 1991. Denil fish ladders were fitted to both of the headgates. Self-powered, self-cleaning fish screens with 1/8 diameter screen size were installed in both canals immediately below the point of diversion. To improve the efficiency of the canal at the upper diversion, an impervious 12 mil rubber/fiber liner was placed 12 inches underground over the entire length of the canal.

	During and after installation of a rubber/fiber liner.

An annual 8,663 acre feet of salvage water, ranging from 6 cfs at base flow to 37 cfs during runoff periods, is also being leased for instream flows during the irrigation season.

This project is designed to benefit bull trout and cutthroat trout by improving connectivity between the upper and middle stream reaches, improving flows for two miles of dewatered stream, reducing loss of fish to irrigation canals, improving riparian plant communities previously affected by dewatering during the growing season.

Fish Populations

In September of 2001, we resampled fish populations at mile 12.0, downstream of the diversion. We recorded significant changes in westslope cutthroat trout and minor changes in bull trout. In 1997, prior to restoration efforts, the Catch Per Unit Effort (CPUE) for young-of-the-year (YOY) westslope cutthroat trout was 0.7 fish/100 feet, compared to 7.7 fish/100 feet in 2001.  CPUE for age 1+ westslope cutthroat trout was 2.5 fish/100 feet in 1997 and 14.3 fish/100 feet in 2001.  In 1997, we recorded no YOY bull trout in this section; in 2000 we picked up our first YOY bull trout in this section. The 2001 surveys indicate that both native species continue to respond to increase flows, fish passage and ditch screening.

Other current projects to improve the fishery in the Cottonwood Creek watershed include implementing rotational grazing systems, removal of stream-side livestock corrals, removal of under-sized culverts and replaced with open-bottom box culvert, purchase of 4,000 acres of Conservation Easements along Cottonwood Creek and a graduate study on whirling disease as it relates to habitat types.