This dataset is a digital elevation model (DEM) of the bathymetry for six sites where known rock structures exist in the St. Croix River. The DEMs have a 10-cm resolution (Boom site is 0.5-m) to provide ultra-high-resolution elevations for investigating the use of hydroacoustic technologies for quantifying habitat for imperiled mussels Spectaclecase (Margaritifera monodonta) and Salamander (Simpsonaias ambigua) typically associated with rock structures (e.g., wing dams, revetment) in rivers. Bathymetry is essential for providing the depths and shapes of underwater terrain and it represents the three-dimensional features (or relief) of underwater terrain. Multibeam sonar data were collected using a Norbit integrated wide band multibeam system compact (iWBMSc) sonar unit. Single-beam sonar data were collected using a SonTek Riversurveyor© M9. All hydroacoustic data were collected in early May of 2021, and the DEMs are provided in GeoTiff format.