This paper describes and assesses: (i) the use of a new instrument for the determination of three-dimensional flow velocities in natural rivers, the acoustic Doppler velocimeter (ADV); and (ii) a method for positioning and orienting such measurements relative to a single local coordinate system to relate flow velocity vectors with the bed and water surface. The ADV uses the Doppler shift principle to measure the velocity of small particles, assumed to be moving at velocities similar to the fluid. Velocity is resolved into three orthogonal components, and measured in a volume 5 cm below the sensor head, minimizing interference of the flow field, and allowing measurements to be made close to the bed. A simple method for positioning and orienting the instrument using digital tacheometry is described, and is used to obtain velocity measurements concurrently with measurements of both bed and water surface topography. The paper includes a preliminary field assessment of the ADV by comparing velocity profiles with those generated from Marsh McBirney electromagnetic current meters, and a full field assessment of the position and orientation methodology. These results suggest that the recommended methods in combination with an ADV are able to provide reliable mean three-dimensional velocity field information and accurate bed and surface topography.