In this paper, an improved method based on a mixture of Gaussian and quadrilateral functions is presented to process airborne bathymetric LiDAR waveforms. In the presented method, the LiDAR waveform is fitted to a combination of three functions: one Gaussian function for the water surface contribution, another Gaussian function for the water bottom contribution, and a new quadrilateral function to fit the water column contribution. The proposed method was tested on a simulated dataset and a real dataset, with the focus being mainly on the performance of retrieving bottom response and water depths. We also investigated the influence of the parameter settings on the accuracy of the bathymetry estimates. The results demonstrate that the improved quadrilateral fitting algorithm shows a superior performance in terms of low RMSE and a high detection rate in the water depth and magnitude retrieval. What’s more, compared with the use of a triangular function or the existing quadrilateral function to fit the water column contribution, the presented method retrieved the least noise and the least number of unidentified waveforms, showed the best performance in fitting the return waveforms, and had consistent fitting goodness for all different water depths.