The amplitude, frequency, and direction of Great Lakes water-level changes over the coming decades is uncertain, with the potential for dramatic impacts on coastal ecosystems and the rare species that depend upon them. Whether the trend will be lake-level rise and ecosystem inundation or lake-level recession and potential ecosystem expansion is unclear. Identifying which species and coastal regions are most likely to be impacted by lake-level fluctuations will help focus resources on the most sensitive species and places. We developed a GIS model to predict lake-level changes using outputs from two regionally downscaled climate models and evaluated how those changes affected the total area of coastal ecosystems in Michigan and increased or decreased habitat for thirteen rare plant and animal species. These species represented a wide range of taxanomic groups and habitat requirements. Regions and ecosystems predicted to have significant responses to modeled lake levels, unsurprisingly, tended to be those with shallow near-shore topography or bathymetry such as Saginaw Bay. Our model predicted both habitat loss and gain for most species, depending largely on the climate model. Our results are an initial step toward proactively prioritizing Great Lakes coastal conservation. Future models that explicitly incorporate species demography, invasive species responses, and other ecological complexities will improve the realism of predictions and therefore conservation outcomes.