We present a novel topo-bathymetric laser profiler. The sensor system (RIEGL BathyCopter) comprises a laser range finder, an Inertial Measurement Unit (IMU), a Global Navigation Satellite System (GNSS) receiver, a control unit, and digital cameras mounted on an octocopter UAV (RiCOPTER). The range finder operates on the time-of-flight measurement principle and utilizes very short laser pulses (<1 ns) in the green domain of the spectrum (λ=532 nm) for measuring distances to both the water surface and the river bottom. For assessing the precision and accuracy of the system an experiment was carried out in October 2015 at a pre-alpine river (Pielach in Lower Austria). A 200 m longitudinal section and 12 river cross sections were measured with the BathyCopter sensor system at a flight altitude of 15-20 m above ground level and a measurement rate of 4 kHz. The 3D laser profiler points were compared with independent, quasi-simultaneous data acquisitions using (i) the RIEGL VUX1-UAV lightweight topographic laser scanning system (bare earth, water surface) and (ii) terrestrial survey (river bed). Over bare earth the laser profiler heights have a std. dev. of 3 cm, the water surface height appears to be underestimated by 5 cm, and river bottom heights differ from the reference measurements by 10 cm with a std. dev. of 13 cm. When restricting the comparison to laser profiler bottom points and reference measurements with a lateral offset below 1 m, the values improve to 4 cm bias with a std. dev. of 6 cm. We report additionally on challenges in comparing UAV-borne to terrestrial profiles. Based on the accuracy and the small footprint (3.5 cm at the water surface) we concluded that the acquired 3D points can potentially serve as input data (river bed geometry, grain roughness) and validation data (water surface, water depth) for hydrodynamic-numerical models.