Finding remnant populations of species that are of conservation concern can be difficult, particularly in aquatic habitats. Models of ecological niches can aid in the discovery of refuges. Remnant populations of native freshwater mussels (unionids) have been found in Lakes Erie and St Clair. Our goals were to predict undiscovered refuges in Lake Ontario based on habitat analysis from Lake Erie and to conduct surveys to test those predictions. We built a presence-only model on environmental data including attributes of the benthic zone and shoreline where mussels occurred in Lake Erie. We found a link between small- and large-scale variables related to unionid persistence. Bathymetry, fetch, and shoreline geomorphology contributed most to the model. These variables correspond to local-scale environmental factors important for unionid survival, including presence of vegetation and substrate composition, which explained ∼22% of the variance in presence, abundance, and richness. The model predicted that 0.8% of the near-shore area of Lake Ontario should be habitat for unionids. In surveys at 34 locations on the USA shore of Lake Ontario, we found 1800 unionids of 11 species and showed that areasOntario, a result signifying generality of our model for conservation approaches to freshwater mussels.