Establishing and monitoring population trends is essential for implementing informed and timely management decisions and also for the conservation of threatened species. We examined changes in Nile Crocodile (Crocodylus niloticus) population size and changes in the size–class distribution within the population using aerial and ground survey data from 1971–2009 in the Ndumo Game Reserve (NGR), South Africa. In addition, crocodiles were caught opportunistically for aging, sexing, and tagging. Precision and accuracy of population estimates were affected by water level, season, and the use of different observers. Future surveys should occur in austral winter and at low water levels. The NGR population increased from an absolute abundance of 348 (±3.4; an estimate of precision based on 1 SE) in the early 1970s to maximum absolute abundance of 992 (±58.7) in 1994 as a result of a restocking program initiated in the late 1960s and early 1970s. The population structure is currently skewed towards subadults and adults and the current population is in decline. This is a result of low recruitment levels in NGR, which are unable to sustain the artificially high population size created by the restocking program. Also contributing to this decline is the poaching of crocodiles and destruction of suitable and historical nest sites. Sex ratios were skewed toward females in juveniles and subadults and toward males in adults, while the overall sex ratio in the population was even. The current NGR Nile Crocodile population is estimated at an absolute abundance of 846 (±263). We predict that the NGR Nile Crocodile population will continue to decline in the future as part of the natural process, but the decline will be accelerated on account of poaching, uncontrolled harvesting, and destruction of nesting habitat.