Light Detection and Ranging (LiDAR), a comparatively new technology in the field of underwater surveying, has principally been used for taking precise measurement of undersea structures in the oil and gas industry. Typically, the LiDAR is deployed on a remotely operated vehicle (ROV), which will “land” on the seafloor in order to generate a 3D point cloud of its environment from a stationary position. To explore the potential of subsea LiDAR on a moving platform in an environmental context, we deployed an underwater LiDAR system simultaneously with a multibeam echosounder (MBES), surveying Kingston Reef off the coast of Rottnest Island, Western Australia. This paper compares and summarises the relative accuracy and characteristics of underwater LiDAR and multibeam sonar and investigates synergies between sonar and LiDAR technology for the purpose of benthic habitat mapping and underwater simultaneous localisation and mapping (SLAM) for Autonomous Underwater Vehicles (AUVs). We found that LiDAR reflectivity and multibeam backscatter are complementary technologies for habitat mapping, which can combine to discriminate between habitats that could not be mapped with either one alone. For robot navigation, SLAM can be effectively applied with either technology, however, when a Global Navigation Satellite System (GNSS) is available, SLAM does not significantly improve the self-consistency of multibeam data, but it does for LiDAR.