In this contribution bathymetric uncertainties induced by the use of frequency modulated (FM) signals for multi-beam-echo-sounder (MBES) measurements are quantified and their relevance for MBES bathymetric uncertainty predictions is assessed. When switching to FM, the quality of depth measurements can get deteriorated due to the Doppler effect and baseline decorrelation. The uncertainty due to the former is divided into second-order (imperfectness of the Doppler-range correction) and first-order (effect on beamsteering) effects. The latter also holds for continuous wave (CW) signals. Here, situations of relevance for measurements in the continental shelf and ship dynamics associated to rough and calm sea-states are considered, and the vertical uncertainty induced by the above sources is quantified. The influence of the Doppler effect depends on the sea state, but is found to potentially have a significant contribution to the MBES error budget for both FM and CW [nearly 82% (rough) and 68% (calm) of the total uncertainty]. The effect of baseline decorrelation depends on the actual pulse shape. For the specifications investigated, vertical uncertainties induced by this source are predicted to be larger for FM than that of CW. This is confirmed by a comparison between the modelled and measured effect on depth uncertainties when switching to FM.