Habitat characteristics can have large effects on nest site selection of oviparous vertebrates. It is thought that habitat preference in many species is driven by natural selection because of habitat-specific fitness consequences. However, long-term studies on nesting of oviparous reptiles, in particular, are less common in comparison with other nesting vertebrates. As a result, specific habitat associations that define nesting habitat for many species are largely unknown. We studied habitat characteristics and selection of American Alligator (Alligator mississippiensis) nest sites in inland freshwater wetlands. We investigated the habitat characteristics associated with 112 nests studied during the 2013–2019 nesting seasons, and quantified habitat characteristics in relation to nest locations and random points. A nearest neighbor analysis indicated that American Alligator nests are not randomly distributed across wetlands, but are more representative of a clumped spatial distribution, suggestive of habitat preference and site selection. We measured habitat variables such as wetland vegetation cover, average water depth, island density, bank slope, canopy cover, and wet bulb globe temperature, as well as alligator population demographics such as relative adult proportion, at each nest and random site. Subsequently, we found that the best variables for predicting American Alligator nest site selection included island density, slope of bank, canopy cover, and wet bulb globe temperature. The best predictive model demonstrated that the odds of nest site selection increased with increasing canopy cover, wet bulb globe temperature, island density, and decreasing bank slope. These habitat choices presumably reduce the risk of nest predation and provide thermal cover for proper balance of nest site microclimate. Based on our results, practices focused on alligator nesting habitat should consider these specific habitat characteristics in outlining applied strategies and working toward management and conservation goals.