Bathymetric LiDAR data from the upper Sacramento River in northern California were acquired September 10-17, 2017, to support research on remote sensing of rivers, particularly mapping water depth, and to facilitate efforts to characterize salmon habitat conditions and geomorphic change along the upper Sacramento River. These data were collected using a Riefl VQ-880-Gairborne laser scanning system designed for combined hydrographic and topographic surveying. The flight was conducted by Quantum Spatial, Inc. (QSI); QSI also performed all processing of the raw LiDAR data. The data were acquired from fixed wing aircraft and were used to produce tiled point clouds in a .las format and interpolated topo-bathymetric raster Digital Elevation Models (DEM's) with a 1 m cell size in an Arc GRID format. The rasters provided in this data release are subsets focused on the reach of the Sacramento River where it is joined by its tributary Cottonwood Creek; supporting field data from this reach were collected in coordination with the acquisition of the remotely sensed data. Three files based on the LiDAR coverage are included in this data release: 1) a topographic DEM with water surface elevations in the channel; 2) a bathymetric DEM with channel bed elevations; and 3) a depth map produced by subtracting the bathymetric DEM from the topographic DEM to calculate the depth as the difference between the water surface elevation and the bed elevation. These data sets are provided as ENVI format files with associated header files.