Advances in topobathymetric LiDARs could enable rapid surveys at sub‐meter resolution over entire stream networks. This is the first step to improving our knowledge of riverine systems, both their morphology and role in ecosystems. The Experimental Advanced Airborne Research LiDAR B (EAARL‐B) system is one such topobathymetric sensor, capable of mapping both terrestrial and aquatic systems. Whereas the original EAARL was developed to survey littoral areas, the new version, EAARL‐B, was also designed for riverine systems but has yet to be tested. Thus, we evaluated the ability of EAARL‐B to map bathymetry and floodplain topography at sub‐meter resolution in a mid‐size gravel‐bed river. We coupled the EAARL‐B survey with highly accurate field surveys (0.03 m vertical accuracy and approximately 0.6 by 0.6 m resolution) of three morphologically distinct reaches, approximately 200 m long 15 m wide, of the Lemhi River (Idaho, USA). Both point‐to‐point and raster‐to‐raster comparisons between ground and EAARL‐B surveyed elevations show that differences (ground minus EAARL‐B surveyed elevations) over the entire submerged topography are small (root mean square error, RMSE, and median absolute error, M, of 0.11 m), and large differences (RMSE, between 0.15 and 0.38 m and similar M) are mainly present in areas with abrupt elevation changes and covered by dense overhanging vegetation. RMSEs are as low as 0.03 m over paved smooth surfaces, 0.07 m in submerged, gradually varying topography, and as large as 0.24 m along banks with and without dense, tall vegetation. EAARL‐B performance is chiefly limited by point density in areas with strong elevation gradients and by LiDAR footprint size (0.2 m) in areas with topographic features of similar size as the LiDAR footprint. © 2018 John Wiley & Sons, Ltd.