Big Lost Wild Trout

The Big Lost River is one of several sinks river drainages in northeastern Idaho. It infiltrates completely into the porous volcanic geology of the northern Snake River Plain and has had no surface connection to the Snake River for at least 10,000 years. The Big Lost River formally terminates at the Big Lost River Sinks. However, the river also naturally loses water at the Chilly Sinks above Mackay Reservoir and the Darlington Sinks near Darlington, Idaho because of the porous nature of the valley floor.

Trout are not native to the Big Lost River Basin. When trout were first introduced into the Big Lost River is unclear, but both rainbow trout and brook trout are thought to have been stocked around 1890. Since then, several subspecies of cutthroat trout have been stocked into high mountain lakes and the Big Lost River, as have golden trout, kokanee, brown trout, and grayling. Rainbow trout and brook trout are the primary components of the trout fishery, but Snake River fine-spotted cutthroat trout have been stocked since 2000 because they are thought to be more resistant to whirling disease infection.

Big Lost Subbasin Map

The Big Lost River was once renowned for its trout fishery, but in the 1980’s anglers reported that trout populations were declining and subsequent surveys by Idaho Department of Fish and Game showed continued decline through the mid-1990’s. Harvest by anglers, habitat degradation, water withdrawal, grazing, water quality, whirling disease, and fish stocking have all been implicated in the decline of Big Lost trout populations. Recent fish survey data show that trout populations have rebounded to levels above those in the 1980’s. Compared to the 1980’s, a recent creel survey showed that angler effort has increased but harvest has decreased, reflecting a shift towards catch-and-release angling.

Our CSI analysis incorporated data from the U.S.D.A. Forest Service, Gregory Aquatics, and 2007 fish surveys completed by the Idaho Department of Fish and Game. A complete list of data sources is provided separately.

Key CSI Findings

• Trout densities are generally high except near dewatered stream segments and in marginal tributary habitats
• Much of the Big Lost River Basin is managed as a wild trout fishery, but triploid rainbow trout are stocked into Mackay Reservoir, East Fork, and Wildhorse Creek. Snake River fine-spotted cutthroat trout are stocked into the North Fork and West Fork.
• Whirling disease is prevalent in the basin, but trout are only susceptible at lower elevations
• Watershed conditions are poor along the mainstem where land has been converted to agricultural fields and pastures are maintained by sprinkler irrigation
• The East Fork, Antelope Creek, Pass Creek, Sage Creek, and the mainstem Big Lost are major waters that are 303(d) listed because of sediment, nutrient, streamflow, and temperature problems
• Wild trout are at low risk to the future threats of land conversion and invasive species
• Uncharacteristic wildfires, climate warming, and resource extraction pose the greatest future risk to wild trout in the Big Lost River Basin

Our CSI analysis showed 34 subwatersheds have the potential to support wild trout in at least a very limited capacity. Much of the Big Lost River and its tributaries are managed as a wild trout fishery, reflected in high subwatershed scores for management emphasis. In 2008, triploid rainbow trout were stocked into Mackay Reservoir, East Fork, and Wildhorse Creek. Snake River fine-spotted cutthroat trout were stocked into the North Fork and West Fork to supplement populations established in 2000.

Population densities are highest in the East Fork, upper Antelope Creek, and the mainstem below Mackay Reservoir. They are lowest in marginal tributary habitat and near dewatered segments on the mainstem and lower Antelope Creek. The extent of connected habitat varied but was highest in the upper basin. The size structure of trout populations showed good ratios of small fish (1 to 6 inches) to large fish (>6 inches) in some headwater streams. However, some populations with fewer small fish scored moderately. Size structure was poor where densities were low in marginal tributary habitat, near dewatered stream segments, and just upstream of the Chilly Diversion. The Big Lost River below Mackay Reservoir had many large rainbow trout that likely moved downstream after being stocked into the reservoir.

Whirling disease is prevalent in the basin, and recent research has shown wild trout to be susceptible at warmer temperatures in lower elevation streams in the Basin. Subwatersheds where trout have been shown to be susceptible scored low. Other watersheds scored low because whirling disease is suspected to be present or it occurs in adjacent watersheds.

Habitat Integrity scored high to moderate in higher elevation tributaries of the Big Lost River Basin but low along the lower mainstem. Watersheds of headwater tributary streams are primarily managed by the Salmon-Challis National Forest and protected as roadless areas except along stream corridors. Several tributaries are listed as 303(d) impaired by the State of Idaho because of livestock grazing and water withdrawal impacts to aquatic habitat. The Bureau of Land Management is responsible for the lower elevation shrublands along larger streams. Private land dominates along the lower mainstem where habitat integrity was low because of extensive canal networks that divert water, water diversion structures that disconnect habitat, land that has been converted to pasture and agricultural fields, and streamflows that are disrupted by Mackay Reservoir; the lower mainstem is also listed as 303(d) impaired. The lower Big Lost River is dry most of the year because water is lost to the Chilly and Darlington Sinks and is withdrawn for irrigation. The loss of water from the Big Lost River has increased because landowners have switched from flood irrigation to sprinkler irrigation. Sprinkler irrigation does not result in return flows and lowers the water table, increasing the loss of streamflows into the porous valley floor. Because the CSI is a broad, watershed-scale assessment, habitat integrity indicators may not accurately reflect local instream habitat conditions in upstream watersheds degraded from grazing impacts, such as the East Fork of the Big Lost River.

Most subwatersheds scored high for Future Security. There is low potential for existing unconverted lands to be converted for agriculture. Several watersheds have hundreds of mine claims and have high resource extraction risk. Only two subwatersheds have been identified for future hydropower development. Risk of winter flooding due to climate change is low throughout the basin, but several mid-elevation subwatersheds have a high risk for uncharacteristic wildfires. The lower Big Lost River Basin has high risk to temperature change under a 3°C climate warming scenario. This indicates that streamflows and riparian vegetation must be restored in a way that ensures cooler water temperatures that buffer against a warming climate. Only the Navarre Creek subwatershed scored moderately low for future security because of high risk to resource extraction, energy development, and climate change.

The U.S. Forest Service, Idaho Department of Fish and Game, Gregory Aquatics, and Trout Unlimited have actively been restoring trout habitat in the Big Lost River Basin. Since 2004, fish passage has been provided on six water diversion structures. Riparian vegetation was recently planted along the East Fork of the Big Lost River where there has been a history of grazing impacts in stream habitat. Trout Unlimited recently acquired a 5 cubic feet per second water right for a fish ladder on the Chilly Diversion. Acquisitions of non-consumptive will continue to improve streamflows and reconnect stream segments and populations. Providing large interconnected habitats will increase the persistence of existing wild trout populations to both natural and anthropogenic disturbances.

The wild trout fishery in the Big Lost River is an important socioeconomic and recreational component of communities in and around the Big Lost River Basin. Idaho Department of Fish and Game, the U.S.D.A. Forest Service, Gregory Aquatics, and Trout Unlimited have and will continue to work to ensure this high quality fishery persists into the future.

Prepared by Dan Dauwalter and Kurt Fesenmyer, TU, 6/17/2009

Conservation Strategies Map