Formerly widespread throughout the waterbodies of eastern South Africa, viable Nile crocodile (Crocodylus niloticus) populations are now restricted to three disjunct protected areas in KwaZulu-Natal (KZN), Mpumalanga and Limpopo. Growing evidence suggests that protected populations are declining, including the breeding C. niloticus population at Lake Sibaya in KZN. Aerial surveys were conducted at Lake Sibaya from 2003–2004 and 2007–2009, spotlight counts in 2003 and intensive nesting surveys in 2003 and 2004. Seven adults were counted during the 2009 aerial survey; an 89% decrease from the 1985 count (62 adults) and a decline of 95–98% of the estimated 1970 adult population. Likewise, in 1970 30 nests were recorded, compared to three nests in 2003 and no recorded nests in 2004. The non-hatchling population in 2003 was estimated at 48 individuals and decreased to an estimated eight in 2009. The neighbouring community perceives crocodiles as a threat to their lives and livestock, and increasing human pressures on C. niloticus in the area will probably ensure that the population will not recover naturally. Unless crocodiles are perceived as a useful or somehow beneficial natural resource by the surrounding community, the species faces possible extirpation from Lake Sibaya in the future.