In many jurisdictions, rare species and their habitats can receive protection if species are assessed as being at risk of declining. The assessment process requires data on habitat occupancy as well as identification of threats to a species critical habitat, both of which are difficult to obtain when the species occurs across large spatial scales. Such is the case for Eastern Musk Turtles (Sternotherus odoratus), which are obligate coastal wetland species in the Laurentian Great Lakes. We use data collected between 2003 and 2015 to map occupancy and conditional occupancy for musk turtles in coastal wetlands of eastern Georgian Bay (Lake Huron) to identify threats to resident wetland habitat. Data collected from a synoptic survey of 58 coastal wetlands were used to create occupancy models, estimate detection probability, and to conduct a sensitivity analysis to determine model robustness. We had a 64–71% probability of detecting musk turtles, whenever present in the wetland, and an area under curve value of 0.82 confirmed high model accuracy. Coastal wetlands that supported musk turtles were associated with higher proportions of forest cover, lower densities of roads, buildings, and docks within 1 km of the wetland, and more-variable bathymetric slopes. High conditional occupancy across the majority of our study area indicates that, at present, habitat in eastern Georgian Bay is in good condition; however, land-use alterations and development should be limited to ensure the persistence of this population of musk turtles.