Population decline of the American alligator (Alligator mississippiensis) was observed in Lake Apopka in central Florida, USA, in the early 1980s. This decline was thought to result from adult mortality and nest failure caused by anthropogenic increases in sediment loads, nutrients, and contaminants. Reproductive impairment also was reported. Extensive restoration of marshes associated with Lake Apopka has been conducted, as well as some limited restoration measures on the lake. Monitoring by the Florida Fish and Wildlife Conservation Commission (FFWCC) has indicated that the adult alligator population began increasing in the early 1990s. We expected that the previously reported high proportion of complete nest failure (θ₀) during the 1980s may have decreased. We collected clutches from alligator nests in Lake Apopka from 1983 to 2003 and from 5 reference areas from 1988 to 1991, and we artificially incubated them. We used a Bayesian framework with Gibbs sampler of Markov chain Monte Carlo simulation to analyze θ₀. Estimated θ₀ was consistently higher in Lake Apopka compared with reference areas, and the difference in θ₀ ranged from 0.19 to 0.56. We conducted change point analysis to identify and test the significance of the change point in θ₀ in Lake Apopka between 1983 and 2003, indicating the point of reproductive recovery. The estimated Bayes factor strongly supported the single change point hypothesis against the no change point hypothesis. The major downward shift in θ₀ probably occurred in the mid-1990s, approximately a generation after the major population decline in the 1980s. Furthermore, estimated θ₀ values after the change point (0.21) were comparable with those of reference areas (0.07–0.31). These results combined with the monitoring by FFWCC seem to suggest that anthropogenic habitat degradation caused reproductive impairment of adult females and decreases in θ₀ occurred with the sexual maturity of a new generation of breeding females. Long-term monitoring is essential to understand population changes due to habitat restoration. Such information can be used as an input in planning and evaluating restoration activities.