We present the sensor concept and first performance and accuracy assessment results of a novel lightweight topo-bathymetric laser scanner designed for integration on Unmanned Aerial Vehicles (UAVs), light aircraft, and helicopters. The instrument is particularly well suited for capturing river bathymetry in high spatial resolution as a consequence of (i) the low nominal flying altitude of 50-150 m above ground level resulting in a laser footprint diameter on the ground of typically 10-30 cm and (ii) the high pulse repetition rate of up to 200 kHz yielding a point density on the ground of approximately 20-50 points/m 2 . The instrument features online waveform processing and additionally stores the full waveform within the entire range gate for waveform analysis in post-processing. The sensor was tested in a real-world environment by acquiring data from two freshwater ponds and a 500 m section of the pre-Alpine Pielach River (Lower Austria). The captured underwater points featured a maximum penetration of two times the Secchi depth. On dry land, the 3D point clouds exhibited (i) a measurement noise in the range of 1-3 mm; (ii) a fitting precision of redundantly captured flight strips of 1 cm; and (iii) an absolute accuracy of 2-3 cm compared to terrestrially surveyed checkerboard targets. A comparison of the refraction corrected LiDAR point cloud with independent underwater checkpoints exhibited a maximum deviation of 7.8 cm and revealed a systematic depth-dependent error when using a refraction coefficient of n = 1.36 for time-of-flight correction. The bias is attributed to multi-path effects in the turbid water column (Secchi depth: 1.1 m) caused by forward scattering of the laser signal at suspended particles. Due to the high spatial resolution, good depth performance, and accuracy, the sensor shows a high potential for applications in hydrology, fluvial morphology, and hydraulic engineering, including flood simulation, sediment transport modeling, and habitat mapping.Remote Sens. 2020, 12, 986 2 of 28 UAV-based 3D data acquisition was first accomplished using light-weight camera systems, where advancements in digital photogrammetry and computer vision-enabled automatic data processing workflows for the derivation of dense 3D point clouds based on Structure-from-Motion (SfM) and Dense Image Matching (DIM). Due to advancements in UAV-platform technology and ongoing sensor miniaturization, today compact LiDAR sensors are increasingly integrated on both multi-copter and fixed-wing UAVs, enabling 3D mapping with unprecedented spatial resolution and accuracy. The tackled applications include topographic mapping, geomorphology, infrastructure inspection, environmental monitoring, forestry, and precision farming. While UAV-borne laser scanning (ULS) can already be considered state-of-the-art for mapping tasks above the water table, UAV-based bathymetric LiDAR still lacks behind, mainly due to payload restrictions.The established techniques for mapping bathymetry are single-or multi-beam echo sounding (SBES/MBES), incl...