Bathymetry and topography are crucial points for sustainable management of rivers. In this context, bathymetric LiDAR appears as an adapted technology for river topography with both high data density and acquisition rate. Nevertheless, even if it exists some references of this technique's precision on coastal areas, few exist on continental waters. Today, LiDAR services providers can deliver full waveform LiDAR signals in addition to processed data. In this context, we wanted to analyze efficiency, quality and precision of bathymetric LiDAR data and waveforms on very shallow coastal waters in order to study a transfer of this technology to rivers. In this paper we present our work on the Morbihan bay (France) data set acquired by SHOM (hydrographic and oceanographic service of French navy) on 2005 with SHOALS system providing Raman, infra-red, and green waveforms. This work is focusing on data quality related to the use of Raman, infra-red, and green waveforms in data processing for surface and water bottom topography. In a first time, we computed bottom altimetrical LiDAR data precision on 9 representative very shallow waters (