A key step in generating effective recovery strategies for species at risk is to identify habitat used under a variety of geographic settings. In part attributable to habitat loss and degradation, the Blanding's turtle (Emydoidea blandingii) is considered at risk across most of its range. Because little information for this species exists for the many islands of Georgian Bay, the world's largest freshwater archipelago, we conducted an intensive study on the habitat use of 12 turtles (6 males, 6 females) on a protected island. We used a combination of radio tracking and GPS loggers to determine habitat use during the active seasons of 2011 and 2012. We used aerial imagery to quantify available habitat and used compositional analyses to determine habitat selection. Both sexes used vernal pools and wet forest to move between habitat patches. Females used inland wetlands early in the year and coastal wetlands during the nesting season, whereas males maintained extensive use of inland wetlands during the entire active season. An effective conservation strategy for Blanding's turtles in Georgian Bay must include protection of inland and coastal wetlands, in addition to the surrounding upland matrix and connecting corridors.