Acoustic channel properties in a shallow water environment with moving source and receiver are difficult to investigate. In fact, when the source-receiver relative position changes, the underwater environment causes multipath and Doppler scale changes on the transmitted signal over low-to-medium frequencies (300 Hz-20 kHz). This is the result of a combination of multiple paths propagation, source and receiver motions, as well as sea surface motion or water column fast changes. This paper investigates underwater acoustic channel properties in a shallow water (up to 150 m depth) and moving source-receiver conditions using extracted time-scale features of the propagation channel model for low-to-medium frequencies. An average impulse response of one transmission is estimated using the physical characteristics of propagation and the wideband ambiguity plane. Since a different Doppler scale should be considered for each propagating signal, a time-warping filtering method is proposed to estimate the channel time delay and Doppler scale attributes for each propagating path. The proposed method enables the estimation of motion-compensated impulse responses, where different Doppler scaling factors are considered for the different time delays. It was validated for channel profiles using real data from the BASE'07 experiment conducted by the North Atlantic Treaty Organization Undersea Research Center in the shallow water environment of the Malta Plateau, South Sicily. This paper provides a contribution to many field applications including passive ocean tomography with unknown natural sources position and movement. Another example is active ocean tomography where sources motion enables to rapidly cover one operational area for rapid environmental assessment and hydrophones may be drifting in order to avoid additional flow noise.