The estimation of the impulse response (IR) of a propagation channel may be of great interest for a large number of underwater applications: underwater communications, sonar detection and localization, marine mammal monitoring, etc. It quantifies the distortions of the transmitted signal in the underwater channel and enables geoacoustic inversion. The propagating signal is usually subject to additional and undesirable distortions due to the motion of the transmitter-channel-receiver configuration. This paper shows the effects of the motion while estimating the IR by matched filtering between the transmitted and the received signals. A methodology to compare IR estimation with and without motion is presented. Based on this comparison, a method for motion effect compensation is proposed in order to reduce motion-induced distortions. The proposed methodology is applied to real data sets collected in 2007 by the Service Hydrographique et Océanographique de la Marine in a shallow water environment, proving its interest for motion effect analysis. Motion compensated estimation of IRs is computed from sources transmitting broadband linear frequency modulations moving at up to 12 knots in the shallow water environment of the Malta plateau, South of Sicilia.