Small drone aircraft systems can provide convenient and unobtrusive monitoring of highly sensitive wildlife species and their habitats. Common terns are notoriously sensitive colonial breeding seabirds known for aggressively mobbing intruders. Kouchibouguac National Park (New Brunswick) is home to one of the largest and most critical colonies in North America, counting up to 7,000+ nests. However, the barrier island complex on which it is established is increasingly threatened by climate change and rising sea level. In this project, a small drone proved highly effective at conveniently capturing very high-resolution imagery (3 cm/pixel) of the Tern Islands in which individual terns could be counted, and major habitat classes distinguished using automated image classification techniques. This approach was far less disturbing to the colony than the intrusive ground surveys traditionally employed to monitor the population and habitat. Moreover, systematic comparisons of tern counts in the drone imagery to nest counts carried out on the ground showed a remarkable degree of correspondence.