Three-channel processing structure was proposed to extend the input dynamic range. Each channel is set up with low, middle or high gain according to the echo intensity from different water depth. Afterwards, a data stitching method and a new fitting approach with the combination of pentagonal and Gaussian function are applied to each three-channel waveform to estimate the depth of water. The multi-channel processing structure was verified on the simulated data sets obtained from the existing Wa-LID waveform simulator. The simulated result has shown that the effective input signal is up to 86.9 dB dynamic range in this new processing technique, and the measured depth reaches 26 m. The bias of the bathymetry estimates is ranging from 1.6 to 4.7 cm with the standard deviation better than 1.1 cm. This multi-channel processing technology can be effectively used in ALB.