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FM-modulated signals with pulse compression are used in the new generation of bathymetric multibeam echo sounders in order to reach higher swath while keeping a high resolution. However, the expected performances are not reached on field data. This article discusses two different effects impacting the bathymetric measurement (Doppler effect and baseline decor-relation). Firstly, the Doppler effect from the antenna motion strongly shifts in time the FM signals processed with the matched filter, and induces measurement bias. Secondly, the pulse compression side lobes affect the final bathymetric measurements: since the instantaneous footprint appears wider because of the temporal side lobes, the interferometric signals appear less coherent (due to baseline decorrelation). This results in an increase of the noise level on the interferometric phase which proportionally impacts bathymetric measurement quality. Considering that Doppler effect measurement biases are already taken into account and corrected in the sounder system, the challenge is to improve the bathymetric measurement quality by reducing the pulse-compressed side-lobes level.