Based on the spectral characteristics of water motion velocity influenced by waves, this paper proposed a method for decomposing the wave orbital velocity and the turbulent velocity. With one velocimeter measuring flow velocity in high frequency, this method can decompose the wave and turbulent velocities from the instantaneous velocity and thus turbulent analysis can be made for water motion influenced by waves. According to the validations, the spectral method can be used in wave-turbulent velocity decomposition for not only the regular waves produced in the laboratory flume but also the irregular waves in the field. The results of decomposition were influenced by the frequency-domain settings. When frequency domains were set beyond the wave window, the wave and turbulent velocities could be well decomposed and the settings had less effect on the decomposition. Besides, the velocity sampling rate can also impact the decomposition. With a low sampling rate of velocity measurement, the instantaneous velocity cannot reflect the flow turbulence, leading to the wave and turbulent velocities cannot be decomposed accurately.