Bathymetric LiDAR utilizes a green laser capable of penetrating water and surveying seafloor topography. The intensity of the echo identified as the seafloor carries information about the substrate type. However, besides the reflectance characteristics of the substrate, there are also other influencing factors, including those from the LiDAR system and the environment. The data collected in the 2010 Dongsha atoll bathymetric LiDAR mission is processed and analyzed in this study. The corrections for environmental factors, mainly contributed from the water column that is presented as the inherent optical parameters of water are retrieved from the recorded green laser waveform. Those from the system, such as deviations between the signal receptors or between laser beam angles to each interface, are eliminated with data from IMU (Inertial Measurement Unit), scanner controlling mechanisms, etc. The resulting reflectance from each flight line is compared in the overlap area. The reflectance of the west side strip is subtracted from that of the east side strip. The reflectance is scaled between zero and one. While the mean of the differences is -0.0037, the standard deviation is 0.0436 for the flight line with a flight height of 400 m. The mean and standard deviation are -0.0058 and 0.0272, respectively, with flight height of 300 m. When interpolating the reflectance from the 300 m flight altitude dataset into a surface after subtracting the point measurement from the 400 m flight altitude, the mean and standard deviations are -0.0215 and 0.0382, respectively. This indicates that the consistency among flight lines of the same flight altitude is higher than those from different flight altitudes. A WorldView-2 (WV-2) image is compared with the LiDAR reflectance, and after atmospheric correction, the green band reflectance from WV-2 showed high similarities between the two image types. However, in the deep water region the one derived from LiDAR has much more information content.