Airborne LiDAR bathymetry (ALB) has shown great potential in shallow water and coastal mapping. However, due to the variability of the waveforms, it is hard to detect the signals from the received waveforms with a single algorithm. This study proposed a depth-adaptive waveform decomposition method to fit the waveforms of different depths with different models. In the proposed method, waveforms are divided into two categories based on the water depth, labeled as “shallow water (SW)” and “deep water (DW)”. An empirical waveform model (EW) based on the calibration waveform is constructed for SW waveform decomposition which is more suitable than classical models, and an exponential function with second-order polynomial model (EFSP) is proposed for DW waveform decomposition which performs better than the quadrilateral model. In solving the model’s parameters, a trust region algorithm is introduced to improve the probability of convergence. The proposed method is tested on two field datasets and two simulated datasets to assess the accuracy of the water surface detected in the shallow water and water bottom detected in the deep water. The experimental results show that, compared with the traditional methods, the proposed method performs best, with a high signal detection rate (99.11% in shallow water and 74.64% in deep water), low RMSE (0.09 m for water surface and 0.11 m for water bottom) and wide bathymetric range (0.22 m to 40.49 m).