The U.S. Geological Survey conducted a bathymetric survey of a reach of the Deschutes River near Bend, OR, between Benham Falls and Dillon Falls on July 25, 2016, to support research on remote sensing of river discharge and characterization of habitat for amphibians, particularly the Oregon Spotted Frog. The bathymetric survey data were obtained with an ITER Systems Bathyswath-1 468 kHz multi-beam echo sounder deployed from a customized research cataraft. The Bathyswath Swath Processor software package was used to acquire the raw data, which then were post-processed, filtered, and gridded using the Bathyswath Grid Processor program. The final output file included in this data release consists of gridded depth measurements in a three-column, comma-separated *.csv text file with easting (x) and northing (y) coordinates and depths, all in units of meters; the projection and datum are UTM Zone 10N and NAD83. These field-based depth measurements were used in combination with hyperspectral image data to develop improved methods of estimating water depth via remote sensing.