This dataset is a digital surface model of the roughness for five (of six) sites where known rock structures exist in the St. Croix River. Roughness is the degree of irregularity of the surface and is computed from elevation. Roughness measures will be used 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. The determination of the roughness plays a role in the analysis of terrain elevation data; it’s useful for calculations of the river morphology and physical geography in general. Multibeam sonar data were collected using a Norbit integrated wide band multibeam system compact (iWBMSc) sonar unit. All hydroacoustic data were collected in early May of 2021, and the roughness rasters are provided in GeoTiff format.