Next to the known photogrammetric or acoustic measurement techniques, nowadays LiDAR is a promising option for high-resolution surveys or monitoring of underwater structures in low turbid and shallow waters. The objective of this investigation is to determine the performance of an underwater laser scanner and an air-borne bathymetric laser scanner for mobile data acquisitions. For this purpose, the underwater LiDAR (ULi) from Fraunhofer IPM is installed on a vessel. To enable the registration and georeferencing of the scan data, ULi is added by an Inertial Navigation System (INS) and two GNSS antennas. On the other hand, the air-borne bathymetric laser scanner (ABS) is integrated into an unmanned aerial system (UAS). Both systems are used to survey in the same measurement area to acquire comparable data sets. With the selected measurement settings, both systems can penetrate through water for more than 10 m and are able to resolve small underwater structures. Caused by shorter measurement ranges, ULi offers a point density which is approximately four times higher than the ABS and is able to resolve vertical underwater structures. The advantage of the UAS mounted ABS is that it can survey in shallow areas which cannot be accessed by vessels.