The latest generation of Multibeam Echo Sounders (MBES) uses Frequency Modulated signals (FM) in order to increase the transmitted energy (via the pulse duration increase) while keeping a high resolution thanks to pulse compression (matched filtering). It enables to increase the signal to noise ratio and thus the swath of these systems. However, the expected performance levels are not reached in practise, and bathymetric measurements are paradoxically noisier. This observation has been done on several systems from different manufacturers (ResonTM Seabat 7150, KongsbergTM EM 122, 302, and 710). The work conducted on this thesis aims at investigating the different causes of measurement uncertainties with the use of modulated signals. The first hypothesis is linked to the Doppler effect (caused by the motion of the arrays following the plateform motion: heave, roll, pitch...). A study based on model and simulations of this effect has been conducted towards two aspects: measurement bias and statistics. Nevertheless, it has concluded that the Doppler effect cannot explain the observed performance losses satisfyingly (the measurement biases being already taken into account and corrected, and the loss in term of statistics being insignificant). A second explanation is based on the presence of sidelobes on the pulse compression which contribute as a noise in decorrelating the interferometric signals (baseline decorrelation). The latter has been shown to be the main cause of degradation on bathymetric measurement with the use of modulated signals. Finally, some realistic solutions have been proposed on the filtering or signal shape designs reducing the impact of the sidelobes (theoretical model, simulation and tested on field data for some of them).