In 1978 Flood was appointed Senior Conservation Officer with the Australian Heritage Commission in Canberra, becoming assistant director from 1979 to 1991, where in 1984 she headed the Aboriginal Environment Section.
She also contributed to the World Heritage Listing of Kakadu National Park, the Tasmanian South West Wilderness Area and the Willandra Lakes Region of NSW.
[7][8] Flood has followed a theoretical approach involving the use of recent ethnographic information to reinterpret the evidence of prehistoric archaeological material on the basis that "there have only been minor changes in the "stone-age, foraging, semi-nomadic way of life" of Aboriginal people throughout history".
[17] On these two expeditions she climbed six previously unclimbed peaks of over 20,000 feet and wrote a book telling the story of the ascents and overland drive to India entitled 'Four Miles High'.
[19] Between 1981 and 1992 she led seven expeditions (funded by Earthwatch) to excavate sites and record rock art in Cape York and the Victoria River region of the Northern Territory.