Dataset associated with a published article titled "Assessing Habitat Suitability for Native and Alien Freshwater Mussels in the River Waal (the Netherlands), Using Hydroacoustics and Species Sensitivity Distributions" Abstract: Longitudinal training dams (LTDs) in the river Waal are novel river training structures that protect the littoral zone from the adverse effects of navigation providing new habitats for riverine macroinvertebrates. In order to inform river management and to better understand their ecological value for native and alien mussel species, it is important to assess the habitat suitability of the protected LTD shore channels. We applied spatial hydroacoustics surveys consisting of side-scan sonar (SSS) and acoustic Doppler current profiler (ADCP) of the substrate type, water depth and flow velocity in three shore channels in combination with species sensitivity distributions (SSDs) to predict habitat suitability for native and alien mussel species. SSDs allowed for the prediction of habitat suitability as a potentially occurring fraction (POF) of a species pool. High substrate type, water depth, and near-bottom flow velocity POFs were found for???70%, 100%, and 4?51% of the total shore channel area, respectively, suggesting that shore channels provide suitable habitat for both native and alien mussel species. To enhance the shore channels as habitat for native mussel species, we recommend increasing shallow areas dominated by fine (silt/clay) and sand substrate types with low near-bottom flow velocities (near 0 m/s). In contrast, the total area of hard substrate (e.g., boulders) in the shore channels should be reduced as it strongly favored invasive alien mussel species in our study. Future research should include additional abiotic parameters to enhance the habitat suitability predictions and compare the results for different riverine habitats. The dataset includes raw side-scan sonar data (SideScanSonar folder), ADCP data (ADCP), images of sediment grab samples (Grab Samples folder; Photos) ...