Airborne lidars have been used in shallow sea surveying and mapping. The water depth extraction algorithm is vital in assessing the system’s maximum sounding ability, similar to lasers, receiving telescopes, and detectors. The conventional water depth extraction algorithm processes the single waveform data and measures water depth through the extraction of the sea surface and seafloor positions in the waveform. This method is susceptible to the influence of strong signals from the seawater scattering layer when extracting weak echo signals from the bottom of the deep water, resulting in a decrease in the ability and accuracy of water depth extraction. To address this issue, the one-dimensional echo waveform data was combined into two-dimensional echo intensity images according to the acquisition order. Each column of the image represented an echo waveform, and the gray value of the image corresponded to the intensity of the echo signal. Using the horizontal correlation of the image and through image processing methods such as bilateral filtering and local threshold binarization, the submarine echo signal profile was extracted. This method both improves the extraction ability of seabed echoes and circumvents the interference of scattering layer signals on weak seabed signals while also providing a new data processing method for the combined detection of shallow sea terrain and underwater targets.