We conducted a landscape-based assessment of fish habitat condition for all lakes in Michigan and the Midwest Glacial Lakes Partnership to help identify appropriate actions and set conservation priorities. Partners delineated lake catchment boundaries and buffers, and summarized a suite of landscape variables for all lakes 25 acres or greater. For each lake, we assessed habitat suitability for selected species, stress from current agricultural and urban landuse, and sensitivity of lake habitat and fishes to future climate change. We first developed a model to estimate the seasonal thermal regime of lakes based on mean annual air temperature and lake size. We then developed boosted regression tree models to predict presence/absence of walleye, northern pike, bluegill, coldwater fishes. We then used these models to estimate species distribution patterns and assessed how these patterns will change under future climate change scenarios. Finally, we developed a decision support framework that identifies appropriate management actions given a lake’s landscape condition and vulnerability to climate change. Our assessment can inform habitat conservation decisions by providing users with information on habitat suitability, current and future threats, and appropriate habitat management strategies for 40,000 lakes in the Midwest Glacial Lakes Partnership.