Although he gave great attention to geology and topography, he his greatest interest lay in collecting freshwater molluscs, and in identifying birds. He published his Birds of Assam (1870-1878) and described a number of birds for the first time, some with Arthur Hay, 9th Marquess of Tweeddale. Most of these notes were published in the Journal of the Asiatic Society of Bengal and Godwin-Austen sometimes drew illustrations of the new bird species. He was particularly active in ornithology after 1863, when he was posted in the eastern Himalayas as part of the political mission to Bhutan headed by Ashley Eden. He surveyed the Garo, Khasi, and Jaintia hills, and in 1875 joined an expedition into the Dafla hills. Venturing into anthropology, he described the monuments and customs of the Khasi tribes.