Field-based real-time kinematic (RTK) GNSS surveys of water surface elevation and channel bed topography were collected along the Blue River, focusing on two cross-sections from which remotely sensed data were obtained. These data were used to assess the accuracy of river bed elevations inferred from the ASTRALiTe bathymetric lidar, acquired from an unmanned aircraft system (UAS). These data sets were collected to support research focused on developing innovative methods for non-contact measurement of river discharge based on various forms of remotely sensed data. The RTK GNSS surveys were performed using a local base station and Trimble R8 and R10 receivers while wading the channel at each cross-section. Additional survey points were measured to define the locations of circular targets used as ground control points for geo-referencing the thermal image time series described in a related data release. The survey data were post-processed by performing an OPUS correction of the static observations collected by the base and adjusting all of the survey points accordingly. The survey data were exported to comma-separated text files and the resulting *.csv files contain for each point number a point ID, spatial coordinates, elevations, and a descriptive code. One of the files contains the depths calculated as the difference between surveyed water surface elevations and bed elevations at points within the channel. The other file contains ground control points.