The Kootenai River Fisheries Recovery Investigation is managed by the Idaho Department of Fish and Game and is comprised of four major projects collectively called the Kootenai River Fisheries Recovery Investigations.  Most of the investigations are transboundary in nature and cooperative with various state, federal, provincial, and tribal agencies.  Notable past accomplishments include determination that the fish community in the Kootenai River since Libby Dam has changed to a greater representation of omnivores; the Kootenai River is nutrient poor and that the additions of phosphorus has improved primary production, secondary production and most recently fish biomass; Kootenai River white sturgeon spawning migration can be accurately predicted by river temperature and stage;  micro habitat and spawning locations of sturgeon have been shown (10 or m of water, sand, temp of 8 C or more and velocities of 0.5 m/s) and that about 60 kcfs is necessary to scour sand from existing cobbles and gravels to provide more suitable spawning substrates; sturgeon spawn first at Shorty's Island and as the season progresses move further up stream but also with high discharge; sturgeon adults are perishing at about 9% a year with only about 10 new recruits a year and that within 20 years the population will be extinct, with mitigated flows sturgeon spawn but the spawning substrate is unsuitable for satisfactory incubation and rearing, PVA studies suggest that at least 210 recruits each year are now necessary to recover the population in 25 years; burbot travel rate, migration and spawning is dictated by discharge with high discharge>12 kcfs during winter impairing burbot spawning, also warmer winter temperatures are delaying migration and may have disrupted burbot maturation and spawning synchrony PVA studies have also been accomplished for burbot rehabilitation with an interum goal of 5,500 fish and an ultimate goal of 17,500; bull trout numbers are stable but low spawning primarily in Calahan creeks; rainbow trout recruitment and growth is low and that there are at least two life history forms with adfluvial fish in the Deep Creek drainage and primarily fluvial fish above Bonners Ferry, Boulder Creek in Idaho is the most important tributary to rainbow recruitment but about 50% of the adults spawn in Montana tributaries.  These accomplishments and more are also found in more than 35 annual reports and about18 peer reviewed publications with several more in progress.  Also, included in the investigation is the cost of restoring Smith Creek to it's natural channel and rejoining the Kootenai River and habitat work on several tributaries that have barriers to rainbow trout spawning.

1) First the white sturgeon measures were taken to rehabilitate the Kootenai River white sturgeon population, an endangered species, the goal is to rehabilitate sturgeon to a fishable level and remove them from the ESA list.  The FY8 goals and tasks will focus on assessing the management application of the "Pilot Project" site and woody material each is or will be in a high use spawning site with the objective of recovery for white sturgeon, the Pilot Project is the first phase of habitat enhancement of a sturgeon spawning site to improve incubation and rearing habitat.  Adult sturgeon will have VEMCO transmitters implanted and their activity around the proposed site will be determined to document Pilot Project use.   This will provide information for future habitat enhancement work. In Aug of 2006 the USACE initiated the Pilot Project by placing  large rock in the Kootenai River at this spawning site.  A stratified random sampling method will be used to statistically document the use of the Pilot Project for the second year and compared to other spawning locations, non-spawning locations and preferred spawning locations.  This will be done through a series of sampling techniques at each early life stage.  Also, juvenile sturgeon will be sampled to identify the success of recovery measures by the USACE as mitigation for sturgeon spawning and recruitment.  Further, juvenile wild and hatchery sturgeon will be sampled in July and August to determine hatchery sturgeon survival and contribution of wild sturgeon from previous mitigation measures by the USACE and BPA.  There will also be an evaluation of a very substantial laval release.

2) A burbot (a species of special concern) investigation in FY10 is designed to determine the management application of measures through a Conservation Strategy to rehabilitate burbot and it is undertaken each fall and winter.  This Goal to is to rehabilitate burbot to a fishable level.  Burbot are winter spawners and the most important measures are designed to improve spawning migration by reducing temperature and discharge in the river.  The capture of adults pre and post spawn and biopsies provides vital information on whether or not these measures result in spawning.  Larval tows are made and light traps are set to search for evidence of spawning success with the capture of larva.   An experimental release of burbot larva in a small pond in the Kootenai basin had moderate success.  But larvae released in a pen in the same pond had 78% survival in 08 and about 40% in 09.  Draining of the pond revealed an estimate of about 99 burbot fingerlings were reared by the begining of September 2008.  Burbot will be sampled at the larvae stage and growth measured. The purpose would be to rear burbot extensively and release them as fingerlings in the Kootenai River for a recovery measure which was done in 09.  In 20010 we will determine the fate of those released and release more burbot.  Also important will be a population viability study to help address the numbers of burbot needed and natural recruitment to achieve a population goal of 5,500 burbot or a high of 10,000.  

3) Ecosystem nutrient restoration to restore nutrients to the Kootenai River was first undertaken in FY05 with a goal to improve primary production lost to the nutrient sink affect of Lake Koocanusa.  The Kootenai River is the largest river in the world that nutrients are purposely being added to to restore primary production and fish growth and survival.  The main objective is to measure the response at the various trophic levels, this is a cooperative investigation with the Kootenai Tribe of Idaho.  The main tasks will involve not only calculating P and N releases and the precise ratio needed daily but biomonitoring of all food transfer levels from algae to the fish community.   Results in FY05, through 09 showed great promise to improve primary production, secondary production, and fish biomass.  Under the nutrient restoration program, mountain whitefish are being studies in particular as an indicator species of ecosystem health before and after nutrients are added.  In 2009 the trout studies were combined with the addition of winter rainbow trout telemetry.