Waterholes are a limited resource vital to the conservation of biodiversity in arid ecosystems. Given the rarity of natural waterholes in deserts and their presumed importance to Vulnerable Nubian ibex Capra nubiana, we examined the influence of landscape characteristics and anthropogenic factors on ibex presence at waterholes. Our results suggest that anthropogenic factors play a larger role in waterhole use than landscape characteristics. Ibex used waterholes regardless of maximum waterhole diameter, maximum water depth or width of the valley in which the waterhole was located. However, ibex were significantly more likely to use waterholes that were far from human dwellings and that had not been visited recently by feral donkeys. Waterhole and ibex conservation will require working with local communities to protect, and ensure sustainable use of, this vital resource.