The lack of information on what constitutes suitable habitat for native freshwater mussels can limit restoration efforts. While many species reside in soft substrates, species such as Cumberlandia monodonta and Simpsonaias ambigua are thought to be associated with rock structures (e.g., wing dams, rock outcrops) in rivers. Our objective was to assess if hydroacoustic technology could be used to quantify physical habitat features for these species. To describe physical habitat, multibeam echosounder, acoustic Doppler current profiler, sidescan sonar, and underwater videography were used to quantify water depth, hardness, bed roughness, and topographic slope of the riverbed, velocity, shear velocity, and the degree of rock clustering at six sites in the Saint Croix River, Minnesota. Despite weak associations between physical habitat conditions and mussel abundance in this pilot study, future refinements in hydroacoustic methods and post-processing computations could improve predictions. Information on habitat features from occupied and unoccupied sites could help resource managers characterize existing occupied habitats, identify potential reintroduction areas, and implement restoration programs.