The lack of information on what constitutes suitable habitat for native freshwater mussels can limit restoration efforts. While many species reside in silt–sand–gravel substrates, species such as the Spectaclecase (Cumberlandia monodonta) and Salamander (Simpsonaias ambigua) mussels are thought to be associated with rock structures (e.g., wing dams and rock outcrops) in rivers. Our objective was to assess if hydroacoustic technology could be used to quantify physical habitat features for C. monodonta and S. ambigua. Multibeam echosounder, acoustic Doppler current profiler, sidescan sonar and underwater videography were used to quantify water depth, substrate hardness, bed roughness and bed slope of the riverbed, water velocity, shear velocity and the degree of rock clustering at six sites in the Saint Croix River, Minnesota. The sites varied in type of rock structures and relative abundances of both species. The strength of the associations among physical habitat features and mussel abundance was weak; R² values were typically < 0.5. However, species-specific differences in microhabitat were observed. For example, C. monodonta was typically observed at sites with higher velocity and shear velocity compared to S. ambigua. Mussel abundance was greatest at sites that contained crevices of sand surrounded by boulders and bedrock. 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 programmes.