A modified Instream Flow Incremental Methodology (IFIM) approach was used on the mainstem Kootenai River from Libby Dam downstream to Bonners Ferry, Idaho. The objective of this study was to quantify changes in habitat for the target fish species, bull trout (Salvelinus confluentus) and rainbow trout (Oncorhynchus mykiss), as a function of discharge in the river. This study used physical data and habitat use information from previous studies in the 1990s. The present study adapted the one-dimensional physical data into a georeferenced data set for each study site. The hydraulic simulations were combined with habitat suitability criteria in a GIS analysis format to determine habitat area as a function of discharge. Results of the analysis showed that the quantity of suitable habitat is greater at lower discharges than higher discharges and that the more stable flow regime from 1993 through 2002 provided more stable habitat conditions when compared to the highly variable flow regime from 1983 through 1992. The daily and weekly variability under 1983-1992 conditions forces subadult bull trout to use less productive habitat during the night by repetitively wetting and drying stream channel margin area. Subadult bull trout exhibit a distinct difference between daytime and nighttime habitat use (Muhlfeld 2002). These fish utilize deeper main channel habitats during the day and move to shallow channel margin areas at night. The productivity of lower trophic levels is low within the consistently watered and dewatered marginal areas and thus these areas provide little foraging value to subadult bull trout that utilize those areas as flows increase. The more stable flow regime (for weekly or daily timesteps) from 1993-2002 should be more productive than flow regimes with high weekly or daily variability. The highly variable flows likely stress subadult bull trout and rainbow trout due to the additional movement required to find suitable habitat or through the utilization of less suitable habitat when more suitable habitat is not available. The GIS approach presented here provides both a visual characterization of habitat as well as Arcview project data in the distribution cassette disk that can be used for additional analysis of flow regimes and spatial variability of habitat within the two sections of the river. The habitat time series can be used to compare habitat changes over time. If a more detailed description of habitat use is required for species such as white sturgeon, it is recommended that new sites using two-dimensional models in critical habitat areas be developed. Based on the habitat characteristics shown in this study, three study sites, one in each section, each approximately 1 mile long could be used to represent the habitat conditions in the Kootenai River.