Animals that experience significant morphological changes throughout their ontogeny often require different habitats at different stages of their lives. The American alligator (Alligator mississippiensis) is an excellent example of such a species, because individuals may increase in size by several orders of magnitude over their lifetime, and this growth is accompanied by changes in their physiology, diet and predator guild. These ontogenetic shifts have been linked to differential habitat use across sex and size classes of alligators in large marsh systems of the Coastal Plain. However, while the majority of studies on alligator ecology have taken place in large contiguous marshes and reservoirs, those habitats comprise a small percentage of the alligator’s total geographic range. We studied an inland population of alligators in the longleaf pine-wiregrass region of southwestern Georgia and found that, in the absence of large bodies of water, alligators used both riverine and seasonal wetland systems. Importantly, different sex and size classes used the two habitats differently. Intensive trapping in the two systems showed that larger animals, and adult males in particular, were primarily captured in the riverine system. One year of radio telemetry further showed that adult males stayed in the riverine system throughout the year. Sub-adults and adult females, on the other hand, were not only captured in both seasonal wetlands and the riverine system but also made overland movements between them. Additionally, we observed nine nesting events in two years in seasonal wetlands and none in the nearby riverine system. Findings from this study indicate that seasonal wetlands may provide critical nesting and nursery habitat for alligators in the inland part of their range. Further, the use of multiple wetland patches within a matrix of upland habitat illustrates the importance of conserving heterogeneous landscapes that can support animals with complex life histories.