Bathymetric Lidarprovidesa practical tool for surveying shallow water zone and the area characterized with navigation threats. The backscatter intensity of laser pulses starting from the emission, and then traveling through air and water, to finally reflected from the bottom, is detectedand recorded. This forms waveform. From the timestamps of feature points in the waveform, the corresponding position and depth can be derived. In thisstudy, the waveforms collected from a Dongsha atoll mission with AHAB Hawkeye II systemare investigated. This system has four receiving channels including two greens, one infra-red and one Raman. Waveforms of different depth, ranging from less than 1m to 40m, are selected for the study. Ensemble Empirical mode decomposition (EEMD) method is used to reduce the noises in the waveform. Weibull distribution is used for fitting the filtered waveform for extracting features. The depths are then derived from the time interval between surface and bottom feature points. The resultis compared with the depth derived from the AHAB Coastal Survey Studio (CSS) software. The moment of laser beam reached water surface could be detected from all these four channels. It is found that there is a time offset among them. This may be caused by the different settings of the detection devices between different channels, such as the length of the signal transmission cable. These offsets certainly should be calibrated in a lab environment.