A method to quantitatively characterize the bed forms of a large river and a preliminary test of the relationship between bed-form characteristics and catch per unit area of benthic fishes is presented. We used analog paper recordings of bathymetric data from the Missouri River and fish data collected from 1996 to 1998 at both the segment (???101-102-km) and macrohabitat (???10-1-100-km) spatial scales. Bed-form traces were transformed to digital data with image analysis software. The slope, mean residual, and SD of the residuals of the regression of depth versus distance along the bottom, as well as mean depth, were estimated for each trace. These four metrics were compared with sinuosity, fractal dimension, critical scale, and maximum mean angle for the same traces. Mean depth and sinuosity differed among segments and macrohabitats. Fractal-based measures of the relative depth of bottom troughs (critical scale) and smoothness (maximum mean angle) differed among segments. Statistics-based measures of the relative depth of bottom troughs (mean residual) and smoothness (SD of the residuals) differed among macrohabitats. Sites with shovelnose sturgeon Scaphirhynchus platorynchus were shallower and smoother than sites without shovelnose sturgeon. When compared with sites without sicklefin chub Macrhybopsis meeki, sites with sicklefin chub were shallower, had shallower troughs, and sloped more out of the flow of the river. Sites with sturgeon chub M. gelida were shallower, had shallower troughs, and were smoother than sites without sturgeon chub. Sites with and without channel catfish Ictalurus punctatus did not differ for any bed-form variables measured. Nonzero shovelnose sturgeon density increased with depth, whereas nonzero sturgeon chub density decreased with depth. Indices of bed-form structure demonstrated potential for describing the distribution and abundance of Missouri River benthic fishes. The observed fish patterns, though limited, provide valuable direction for future research into the habitat preferences of these fishes.