Fish and wildlife resources in the Kootenai drainage were historically abundant and were used by the Kootenai Tribe for cultural and subsistence purposes. Over the past decades, native fish and wildlife populations have declined significantly due to large-scale habitat and ecosystem changes. The Kootenai River White Sturgeon Study and Conservation Aquaculture Project was initiated by the Kootenai Tribe of Idaho as a stopgap measure in 1989 to produce fish from wild Kootenai River adults until effective habitat restoration measures could be identified and implemented.

Upon completion of the new Twin Rivers Sturgeon and Burbot Hatchery and the upgrades to the Kootenai Tribal Sturgeon Hatchery during 2013-2019, several major milestones were reached and several annual activities were advanced after years of planning.
•    Upgrading the Kootenai sturgeon production facilities at the existing Tribal Sturgeon Hatchery near Bonners Ferry, Idaho. Developing a new artificial production facility for Kootenai sturgeon and burbot at the confluence of the Moyie and Kootenai Rivers (Twin Rivers Sturgeon and Burbot Hatchery).
•    Collecting and incorporating an increased number of native Kootenai sturgeon broodstock from the Kootenai River to increase genotypic and phenotypic diversity.
•    Collecting and incorporating an increased number of native burbot broodstock from within basin sources (i.e. Moyie Lake stock from British Columbia) and from the standing stock of hatchery-reared surviving adults in the river to increase genotypic and phenotypic diversity.
•    Spawning, incubating, and rearing an increased number of Kootenai sturgeon and burbot families, and also in a manner whereby RM&E may utilize Parental-Based Tagging of distinct “family groups” to monitor post-release survival, growth, maturation, and dispersal.
•    Hatchery production of burbot supports an adult abundance that has allowed for opening a fishery.
•    Refining aquaculture techniques for sturgeon and burbot.
•    Releasing Kootenai sturgeon and burbot at appropriate developmental stages to habitats in the Kootenai River to evaluate habitat related recruitment dynamics / recruitment failure.
•    Supporting operations and monitoring at both facilities.

White Sturgeon Conservation Aquaculture Summary:

Aquaculture techniques were applied to the Kootenai River white sturgeon population in response to concerns that missing year classes, failed recruitment, and skewed age class structure were threatening this population with extinction. An independently produced conservation breeding plan to preserve the population's remaining genetic variation was implemented in 1994 (Kincaid 1993). The population was listed as endangered under the Endangered Species Act (ESA) in 1994 (USFWS 1994), due to unmitigated population decline and predominant recruitment failure on a decadal scale.

A USFWS Recovery Plan for the population was completed during 1999 (USFWS 1999), and recently updated during 2019 (USFWS 2019). Subsequent concerns regarding duration, breadth, and magnitude of Kootenai River ecosystem degradation in Montana, Idaho, and British Columbia, and repeated failure to restore natural recruitment during the past decade suggested that a conservation hatchery program was warranted to preclude extinction. Without hatchery intervention, population extinction is certain during the next 20-40 years. With intervention, assuming ongoing natural recruitment failure, this hatchery program will contribute to demographic restoration and protection of remaining genetic variability during the next 30 to 50 years, while improvements in the Kootenai River ecosystem occur to collectively reestablish natural production and ecological function. The Kootenai River White Sturgeon Conservation Aquaculture Program has expanded since the initial implementation of the Kincaid Plan in 1994. Since then, the Program has: 1) produced, released, and monitored frequent year classes of captive-reared progeny from wild, native brood stock, 2) continued to preserve within-population genetic diversity, 3) minimized disease introduction and transmission, and 4) substantially contributed to the developing field of white sturgeon conservation aquaculture.

The program is designed to preserve the locally adapted Kootenai River white sturgeon genotypes, phenotypes, and associated life history traits and restore age class structure to maximize future population viability and persistence.  In the future, Parental Based Tagging may provide methods to evaluate habitat dynamics through experimental early life stage releases similar to the Burbot Program. The program incorporates an adaptive management approach and will be modified as necessary, following collection and analysis of the most recent and most complete empirical datasets. These datasets will then be used in updated ecosystem, demographic, and genetic models to guide the Program and maximize its effectiveness and success, in the broader context of Kootenai River ecosystem restoration. The sturgeon aquaculture program has released >300,000 juveniles from 24 year classes to date, resulting in a hatchery-reared juvenile population of 12,000-15,000 individuals aged 1-25 years old and dispersed from Montana to Kootenay Lake.  During 2020, the first sexually mature hatchery-reared sturgeon were captured, two mature males.  Monitoring genetic diversity continues, and diversity of year classes has represented the genetic diversity potential of the wild spawning adult population.  The Sturgeon Program also continues to monitor Spontaneous Autopolyploidy.  During 2015-2019, both Kootenai Tribal Hatcheries were rearing sturgeon. The number of sturgeon families making up the 2015 year class increased to 27, and then the 2016-19 year classes increased to 29-36 per year. This was an increase from an average of 15 through 2014. Under co-manager agreement, half of each sturgeon family are being reared on an accelerated growth (warm water) regime, and half of the fish on the ambient Kootenai River water temperatures. Twin Rivers has the capability for the accelerated growth temperature regime, increasing probability of post-release survival. Although survival of fish reared on Kootenai River ambient water have a lower post-release survival, they may have adaptability advantages in the long-term. This remains to be determined, but rearing a portion of each family on the two temperature regimes increases the probability of one or both strategies proving successful in the long-term.

Burbot Conservation Aquaculture Summary:

Native Burbot (Lota lota) in the Kootenai River in Idaho were petitioned for ESA listing, are Red Listed in B.C., and are a designated species of special concern in Idaho and Montana. It is believed that at one time, the burbot fishery in Idaho and British Columbia produced many thousands of fish each winter. Tribal elders report that burbot (ling) were extremely abundant in the Kootenai River in Idaho and were a main staple for the Tribe in the late winter/early spring months. The Kootenai Tribe relied heavily upon this important subsistence fishery and tribal members were very adept at using weirs and traps. Burbot also provided a valuable social, sport, and commercial fishery but the fishery collapsed soon after the completion of Libby Dam. Burbot were once very important to the anglers of Kootenay Lake, as well. Just as in Idaho, the Canadian fishery collapsed soon after Libby Dam began operations.

Overexploitation of burbot in Kootenay Lake and Kootenai River was a concern for fish managers when it became evident the fishery was at risk of failing. Measures were taken to reduce exploitation by reduction in creel limits and fishery closures but none of these measures restored the fishery. Examples of stock rebound in overexploited burbot populations with fishery restrictions or closures have been documented, although habitat was generally intact in such cases. Operation of Libby Dam for hydropower (including power peaking) and flood control during the winter months has resulted in more erratic flows that are up to 6-fold higher than pre-dam conditions and warmer winter water temperatures. In addition, Lake Koocanusa, the impoundment created by Libby Dam, acts as a nutrient-sink and has reduced productivity of the river. Potential threats to the population include: current winter flow management, power peaking, changes in river temperature, loss of slough and side-channel habitat from diking, nutrient loss, and spring management of Kootenay Lake. An investigation was initiated by IDFG in 1993 to assess burbot abundance, distribution, size, reproductive success, and movement, and to identify factors limiting burbot in the Kootenai River in Idaho and British Columbia.  Then, in 2002, KTOI convened a burbot recovery committee of local stakeholders and scientists from agencies in the Kootenai/y drainage to identify and implement conservation strategies to help alleviate threats to the species. Conservation strategies identified in the recovery plan for burbot include: ecosystem recovery, development of a winter flow plan, spring management of Kootenay Lake levels, use of donor stocks, captive broodstock and culture. As with white sturgeon, conservation aquaculture will play a positive role in the recovery of this species, while efforts to restore habitat conditions necessary for the survival and natural production of burbot continue.  A Memorandum of Understanding signed by the participating management agencies and stakeholders defines the commitment of the participants to implement the conservation strategy to restore burbot in the Kootenai/y drainage. Through this project, culture techniques for native burbot have been developed and refined, in cooperation with the co-managers and U of I.

Native burbot in the Idaho and Canadian portion of the Kootenai River drainage are still at risk of becoming extinct if hatchery production were to cease.  The outlook for burbot recovery is promising.  Co-manager RM&E results indicate hatchery-reared juvenile burbot can survive, may grow significantly, mature, spawn, and resulting in a low but identifiable amount of natural recruitment. Thus, the next steps are to continue producing/releasing year classes; to determine early life stage post-release survival / bottlenecks; and to increase natural recruitment.  The partial release of each year class across all early life stages across different habitats in Idaho and BC has allowed the program to simultaneously evaluate recruitment bottlenecks and meet restoration objectives for substantial population rebuilding. The 2015-2019 burbot rearing at Twin Rivers Hatchery resulted in releases of ~1,400,000 juveniles and several million larvae for population rebuilding and release strategy evaluation in Idaho and BC.