The major Nile crocodile Crocodylus niloticus populations in South Africa are threatened by pollution, habitat alteration/destruction, and poaching. This has highlighted the importance of other minor populations. The Phongola River Nile crocodile population was previously considered as unsubstantial. Consequently, we investigated the Nile crocodile population numbers and status and the effects of the impoundment of the Phongola River on this. In 2009–2010 we determined a minimum population number of 281 Nile crocodiles in Pongolapoort Dam using a combination of survey methods. The population structure was identified as having a minimum of 116 (41.3%) juveniles (<1.2 m total length), 31 (11.0%) subadults (1.2–2.5 m total length) and 134 (47.7%) adults (>2.5 m total length). At the commencement of the breeding season in August, crocodiles congregated at a major basking site where the main tributary entered the dam. Three major nesting areas were identified, two of which were located on the river inlet to the dam. We identified approximately 30 nesting females during the 2009/10 nesting season. Several nests were predated by the Nile monitor Varanus niloticus. There was a total recruitment failure of nests along the river inlet to the dam due to a flash flood of the Phongola River in January 2010. This preliminary study suggests that the Pongolapoort Dam Nile crocodile population has a relatively high potential reproductive output, although their annual successes may vary greatly because of loss of nesting sites as a result of water-level fluctuations and predation. It appears that the river impoundment has generally had a positive impact on this Nile crocodile population, although suitable nesting sites may become limited. Continued long-term monitoring of the Nile crocodile population in Pongolapoort Dam is required to determine if the impoundment continues to support a viable population.