This work introduces a new method to calculate the water velocity components of a turbulent water column in the x, y, and z directions using Autonomous Underwater Vehicle (AUV) motion response (referred to as the ‘WVAM method’). The water column velocities were determined by calculating the difference between the motion responses of the vehicle in calm and turbulent water environments. The velocity components obtained using the WVAM method showed good agreement with measurements from an acoustic Doppler current profiler (ADCP) mounted to the AUV. The standard deviation between the two datasets were below 0.09 m s−1 for the velocity components in the x, y, and z directions, and were within the uncertainty margin of the ADCP measurements. With the WVAM method, it is possible to estimate the velocity components within close proximity to the AUV. This region encompasses the vehicle boundary layer and the ADCP blanking distance, which is not typically resolved. Estimating vertical and horizontal velocities around the boundary layer of the AUV is important for vehicle navigation and control system optimization, and to fill the blanking distance gap within a water column velocity profile, which is important for flow field characterization. The results show that it is possible to estimate the flow field in the vicinity of AUVs and other self-propelled vehicles.