Freshwater megafauna populations, which are declining worldwide, are well known but often overlooked and understudied compared with marine and terrestrial megafauna. One species of freshwater megafauna is the Suwannee alligator snapping turtle (Macrochelys suwanniensis), which is endemic to the Suwannee River drainage in Georgia and Florida. Several trapping studies have examined M. suwanniensis distribution, body size, and population structure, but little information exists regarding its population status. The objectives of our study were to 1) estimate population size, 2) estimate apparent survival, and 3) model population growth rates (k) by conducting a capture–mark–recapture study of M. suwanniensis in the Suwannee River in Florida. From 2011 to 2013, we repeatedly sampled 12 randomly selected 5-km sites along the Suwannee River for M. suwanniensis using baited hoop-net traps. We captured 126 individuals and had 29 recaptures. Both adult males and adult females had very high apparent survival (0.99), whereas juveniles had lower apparent survival (0.32). We estimated a population density of 6.6 turtles/river km, indicating a population of 1709 (95% CI, 1205–2694) M. suwanniensis from the town of White Springs to the upper limit of the estuary in the main stem of the Suwannee River (approximately 259 river km). We constructed 2 postbreeding census matrix population models for M. suwanniensis and incorporated parameters from this study and from the literature. Both matrix population models suggested a slightly decreasing population (k = 0.99), but because of the uncertainty around our estimates, we consider the population trend to be unclear. Elasticity analysis revealed that k was most sensitive to changes in adult survival compared with other model components. This is a conservation concern because adult M. suwanniensis may be incidentally killed by fishing gear. Our study was short-term, and our analyses had limitations; therefore, we recommend future areas of research, including long-term population monitoring.