The U.S. Geological Survey, in cooperation with the Missouri Department of Conservation, undertook a study to quantify fish habitat by using relations between streamflow and the spatial and temporal distributions of fish habitat at five sites in the Marmaton and Marais des Cygnes Rivers in western Missouri. Twenty-six fish habitat categories were selected for nine species under varying seasonal (spring, summer, and fall), diel (summer day and night), and life-stage (spawning, juvenile, and adult) conditions. Physical habitat characteristics were determined for each category using depth, velocity, and channel substrate criteria. Continuous streamflow data were then combined with the habitat-streamflow relations to compile a habitat time series for each habitat category at each site. Fish habitat categories were assessed as to their vulnerability to habitat alteration based on critical life stages (spawning and juvenile rearing periods) and susceptibility to habitat limitations from dewatering or high flows. Species categories representing critical life stages with physical habitat limitations represent likely bottlenecks in fish populations. Categories with potential bottlenecks can serve as indicator categories and aid managers when determining the flows necessary for maintaining these habitats under altered flow regimes. The relation between the area of each habitat category and streamflow differed greatly between category, season, and stream reach. No single flow maximized selected habitat area for all categories or even for all species/category within a particular season at a site. However, some similarities were noted among habitat characteristics, including the streamflow range for which habitat availability is maximized and the range of streamflows for which a habitat category area is available at the Marmaton River sites. A monthly habitat time series was created for all 26 habitat categories at two Marmaton River sites. A daily habitat time series was created at three Marais des Cygnes River sites for two periods: 1941 through 1963 (pre-regulation) and 1982 through 2003 (post-regulation). The habitat category with the highest median area in spring was paddlefish (Polyodon spathula) with normalized areas of up to 2,000 square meters per 100 meters of stream channel. Flathead catfish (Pylodictis olivaris) habitat area generally was the category area most available in summer and fall. Differences in daily selected habitat area time series between pre- and post-regulation time periods varied by species/category and by site. For instance, whereas there was a decline in the distribution of spring spawning habitat for suckermouth minnow (Phenacobius mirabilis) and slenderhead darter (Percina phoxocephala) from pre- to post-regulation periods at all three sites, the 25 to 75 percentile habitat area substantially increased for paddlefish under post-regulation conditions. Potential habitat area for most species was maximized at the Marmaton River sites at flows of about 1 to 10 cubic meters per second, whereas median monthly streamflows ranged from less than 1 to 20 cubic meters per second depending on site and season. Paddlefish habitat was available beginning at higher flows than other categories (4 to 7 cubic meters per second) and also maximized at higher flows (greater than 50 to 100 cubic meters per second). Selected potential habitat area was maximized for most species at the Marais des Cygnes River sites at flows of about 1 to 50 cubic meters per second, whereas median monthly streamflows ranged from 4 to 55 cubic meters per second depending on site and season. The range of streamflows for which selected habitat area was available in summer and fall was substantially less at the channelized Marais des Cygnes River site when compared to the non-channelized sites, and, therefore, the susceptibility of categories to high-flow habitat limitations was greater at this site. The channelized reach was more unifor