The latest generation of bathymetric multibeam echo sounders (MBES) uses frequency modulated (FM) signals with matched filtering using pulse compression in order to reach wider swath (by increasing the transmitted energy via pulse duration, resulting in a better SNR) while keeping a high accuracy (shorter efficient pulse duration). Practically, this makes possible measurements from deeper seafloor or wider swath where classical pulse shapes (CW) are not working. However, the comparison between bathymetric data from FM and CW systems shows that data from FM signals are often noisier than the one using CW signals. Why this paradoxical observation, since in theory the signal to noise ratio is increased by the matched filtering when using FM ? A first hypothesis for this bathymetric measurement degradation could be the Doppler effect induced by the motion of transmitting and receiving arrays (from roll, pitch, yaw, heave...). The received signal being thus shifted in frequency, it is not adapted anymore to the matched filtering, causing time fluctuations of the detected echoes. A study of Doppler effect impact on FM signal bathymetry has been conducted, concluding that Doppler effect cannot fully explicate bathymetric quality loss observed when using FM signals. Another explanation is that side lobes of the signal appearing after pulse compression play a role in the interferometric phase statistics, considering the angular (or baseline) decorrelation (the bathymetric quality being proportional to the interferometric phase fluctuation level). A modelling study comforted by simulations and field data measures has confirmed this hypothesis. The solution to the issue of performance degradation due to using FM could then be found in an adaptation of the signal design or the processing applied.