Negative human-wildlife interactions can be better managed by early detection of the wildlife species involved. However, many animals that pose a threat to humans are highly cryptic, and detecting their presence before the interaction occurs can be challenging. We describe a method whereby the presence of the estuarine crocodile (Crocodylus porosus), a cryptic and potentially dangerous predator of humans, was detected using traces of DNA shed into the water, known as environmental DNA (eDNA). The estuarine crocodile is present in waterways throughout southeast Asia and Oceania and has been responsible for >1,000 attacks upon humans in the past decade. A critical factor in the crocodile's capability to attack humans is their ability to remain hidden in turbid waters for extended periods, ambushing humans that enter the water or undertake activities around the waterline. In northern Australia, we sampled water from aquariums where crocodiles were present or absent, and we were able to discriminate the presence of estuarine crocodile from the freshwater crocodile (C. johnstoni), a closely related sympatric species that does not pose a threat to humans. Further, we could detect the presence of estuarine crocodiles within an hour of its entry and up to 72 hours after the crocodiles were removed from aquariums. We conclude that eDNA could be a valuable tool for reducing human-wildlife conflict through early detection of the species.