Bathymetric lidar systems, e.g., the Scanning Hydrographic Operational Airborne Lidar Survey (SHOALS) have a proven capability to measure water depth accurately. Although the system is optimized for depth retrieval, there is much more than depth information since the data stream (waveform) includes backscatter from the water surface and water column as well as the bottom return. This paper uses the amplitude of the bottom return signal to characterize the illuminated bottom materials. It is found that, while there are changes in the bottom return that clearly correlate with changes in bottom type, the bottom slope and surface waves have significant effects on the bottom return. These factors can distort the recorded waveforms and alter the apparent reflectance of illuminated materials, and must be accounted for if changes in bottom type are to be detected.