Airborne LiDAR Bathymetry has been proven as an ideal technique for safely and efficiently operating in both shallow water and tidal flat areas for 3-D topographic mapping tasks. Yet the crucial challenge for acquiring terrain of water bottom is to precisely capture the trajectory of laser pulse when travelling between different medium, in the air, water and at the water bottom. Therefore, the quality of mapping 3-D bottom terrain would depend on how well the waveform analysis on determining the timing hitting water surface and water bottom can be designated. The goal of this research is to focus on comprehending the reaction of laser pulse on water surface, mainly wind-induced capillary-gravity wave facets. In particular, laser scanning geometry and the wind factor that shape the waveform geometrically and radiometrically are analyzed and thus the better timing detection method can be advised. It is suggested that adopting 50% risetime point, among others, would render better timing detection results when operating under moderate to strong wind speeds. In addition, when provided with gentle wind speed, bathymetry scanned in a lower off-nadir angle would gain richer energy. Through this study, better understanding of laser-to-water interaction is realized. Last but not least, this work may contribute to highlighting the significance of water surface detection which current airborne LiDAR bathymetric systems overlook.