Sturgeon use benthic habitats in and adjacent to main channels where environmental conditions can include bedload sediment transport and high near-bed flow velocities. Bed velocity measurements obtained with acoustic Doppler instruments provide a means to assess the concentration and velocity of sediment moving near the streambed, and are thus indicative of the bedload sediment transport rate, the near-bed flow velocity, and the stability of the substrate. Acoustic assessments of benthic conditions in the Missouri River were conducted at scales ranging from the stream reach to individual bedforms. Reach-scale results show that spatially-averaged bed velocities in excess of 0.5 m s-1 frequently occur in the navigation channel. At the local scale, bed velocities are highest near bedform crests, and lowest in the troughs. Low-velocity zones can persist in areas with extremely high mean bed velocities. Use of these low-velocity zones may allow sturgeon to make use of portions of the channel where the average conditions near the bed are severe. To obtain bed velocity measurements of the highest possible quality, it is necessary to extract bottom-track and GPS velocity information from the raw ADCP data files on a ping-by-ping basis. However, bed velocity measured from a point can also be estimated using a simplified method that is more easily implemented in the context of routine monitoring. The method requires only the transect distance and direction data displayed in standard ADCP data-logging software. Bed velocity estimates obtained using this method are usually within 5-10% of estimates obtained from ping-by-ping processing. ?? 2007 Blackwell Verlag.