In December 2013, an experiment using an autonomous underwater vehicle (AUV) as a moving source for water column sound speed profile (SSP) inversion was conducted in Mogan Lake, China. With in-situ conductivity, temperature, and depth (CTD) measurements, the empirical orthogonal functions were first constructed to represent the SSP. Radiated noises of the AUV were received on a vertical line array and processed via acoustic field matching to obtain estimates of the range-independent SSP, along with the position and velocity of the AUV and the water column depth. The frequency of the radiation noise of the AUV was approximately 14 kHz. At such high frequency, even though the source motion was slow, a significant Doppler shift/broadening was observed. To incorporate the Doppler effects to better match the measured data, a forward acoustic model is derived based on the waveguide Doppler and normal mode theory. An analytical solution of the forward model is obtained for arbitrary signal integration intervals with a monochromatic source, moving radially relative to the receiver. Through simulations and experimental data processing, the feasibility of using an AUV source for water column SSP inversion has been demonstrated; it is also shown that the waveguide Doppler model is more effective compared with the model that does not consider the waveguide Doppler effect.