Effective management of a species requires that resource managers know critical aspects of its ecology, including information on home range and habitat use. We conducted the first telemetry study on the Suwannee alligator snapping turtle (Macrochelys suwanniensis), and we examined movements at an upper river (UR) site and a lower river (LR) site in the Suwannee River in Florida, USA. We estimated home range size with kernel density estimates (KDE) using the FishTracker GIS toolbox, and we examined potential differences in KDEs with Generalized Linear Models (GLMs). We also used GLMs (family = binomial) to examine habitat selection for M. suwanniensis. We used an information-theoretic approach to rank and select the most parsimonious models. Overall, our models revealed that M. suwanniensis possessed larger 90% KDEs in the LR site than the UR site, and in both sites, turtles moved into the floodplain during flooded conditions. Remarkably, these movements continued even after water levels receded and the aquatic links were severed. Interestingly, M. suwanniensis selected shallow water with some type of subsurface cover, especially large woody debris (LWD). Instream LWD is likely extremely important, especially during low water levels when undercut banks and other bank habitats are unavailable, so the removal of LWD, including deadhead logs, could negatively affect the species. Minimum flows have been established in the drainage, but river water levels have declined an estimated 40% since human settlement, partly because of groundwater withdrawal outside the drainage, potentially imperiling this state Threatened species.