The Niobrara River is a National Scenic River in northern Nebraska. The Niobrara River is characterized by a sand channel with areas of gravel and bedrock. Bathymetric and topographic surveys were completed at five sites (Norden, Meadville, Mariaville, Spencer, and Niobrara) on the Niobrara River in August 2020. The bathymetric data were collected using Acoustic Doppler Current Profilers (ADCPs) attached to kayaks. The ADCP data were collected on transects and between the transects following the flow of the river at each site. Topographic data including water surface elevations were collected with survey grade Global Navigation Satellite Systems (GNSS). A temporary reference point was established at each of the five sites on which a GNSS base station was deployed. Eight to fourteen hours of static satellite observation data were collected over the temporary mark and submitted to the National Geodetic Survey Online Positioning Users Serve (OPUS) to get an accurate horizontal and vertical position on the temporary mark. This corrected position for the base station was used to adjust and correct the rover data (water surface elevations and shallow streambed elevations). Water surface elevations were applied to the data collected along each transect to give a cross-section of streambed elevation from the measured depth. For data collected in between transect lines, a slope model was used to apply water surface elevations to the measured depths to give a longitudinal profile of streambed elevation. At random locations with depth greater than 0.15 meters (m), light intensity measured by a LICOR LI-192 Underwater Quantum Sensor in µmol of photons m^-2 s^-1, Secchi depth m, and turbidity Formazin Nephelometric Unites (FNU)) were measured. The data will be used by the Earth Resources Observation and Science Center (EROS) to evaluate topobathymetric lidar data collected with a Riegl VQ-880-G topobathymetric lidar sensor. The Niobrara River provided environmental conditions with varying degrees of streambed type, water clarity, and depth that were useful in understanding lidar sensor performance. Bathymetric and GNSS survey data were collected during the same day as the topobathymetric lidar data to ensure an accurate comparison because each site had a complete or partial sand streambed. The light intensity, Secchi depth, and turbidity readings will be used to determine water clarity. The water clarity will be used to evaluate the effectiveness of the topobathymetric lidar sensor and assess the conditions that are optimal for the topobathymetric lidar sensor use. Two data files in comma separated values format are included: Niobrara_River_Bathymetry_GNSS_Data_2020.csv which includes streambed elevations from the ADCP and GNSS surveys and Niobrara_River_Light_Secchi_Turb_Readings_2020.csv which includes water clarity data.