Woolnough lectured at Adelaide and Sydney Universities to 1911, and in that year he joined J.A. Gilruth's expedition to the Northern Territory, subsequently publishing an important bulletin on the Territory and a geological map of the northern portion, based on H.Y.L. Brown's earlier work, but with considerable additions by Woolnough.
He became foundation Professor of Geology at the University of Western Australia in 1913, remaining there until 1919. In Western Australia he made major studies of "duricrust", a term he coined, and on other aspects of geomorphology. Woolnough then joined Brunner Mond Alkali company to seek economic salt deposits in Australia. He travelled widely, and despite the physical disabilities that barred him from a place on Scott's polar expedition in 1910, and from war service, he covered vast distances (1 000 miles on foot in seven weeks) in his work. He was not averse to using camel, bicycle, horse or car however.
In 1940, not long before his retirement, Woolnough reviewed the then known iron ore occurrences of Australia for the Commonwealth, and because of the apparent limited supply an embargo (lasting until 1960) was placed on export of iron ore.
After retiring Woolnough carried out consulting for the next ten years, but turned increasingly to bibliographic and translating work, as his health deteriorated, and supported himself by translating scientific articles from more than a dozen languages. The first D.Sc. of Sydney University, he was honoured by numerous other organisations. His name is commemorated in the Woolnough Hills, W.A., the Woolnough Lecture Theatre in the University of Western Australia, the Woolnough Geological Library at the University of New England and a sea-mount south east of Sydney.
Woolnough was one of the first group of honorary members elected by the Geological Society of Australia in 1957.