The geometry of river channels is a key descriptive element for hydromorphology, hydraulics and hydroecology. Gravel bed rivers usually have a mean water depth of a half-metre. For such shallow waters, the accuracy of bathymetric LiDAR data has to be precisely assessed. Alongside this accuracy investigation, methodological questions arise: How to assess the data quality of elevation LiDAR when comparing reference topographic points on river beds to laser beam footprints of several square metres at different locations? What are the consequences of uncertainties and scaling in accuracy estimations? In this study, we designed a methodology to assess the quality of LiDAR topographical data within rivers using a specific geostatistical method that conducts upscaling as well as interpolation of reference data that takes into account uncertainties. This method uses an anisotropic block kriging from DGPS points on LiDAR footprint areas within a channel-fitted coordinate system. This assessment focused on a 1.5 km long reach of the Gardon gravel bed river, south of France. DGPS points pseudo-regularly located along the river were acquired at the same time as the LiDAR survey with the HawkEyeII system. LiDAR accuracy results for river bottom elevation show a negative bias for high depth. Added to that bias, a random error with 0.32 m standard deviation was found by considering upscaling and uncertainties in reference data, and a 0.20 m standard deviation was found if they were not considered. Consequently, if LiDAR bias can be corrected, measuring a water depth less than 32 cm, i.e., for 28 % of the river area, is unrealistic. However, this experiment shows that LiDAR provides an accurate representation of the riverbed forms. It also provided a useful, continuous, topographic surface from the underwater river bed up to riparian areas.