Her early studies were at the South Kensington Schools in London, where, unusually, she was trained in lithography, and also Mission Gann"s Life School. Her first regular employment extending over 7 years, was as commercial artist for the Sydney firms of Gibbs, Shallard & Company and South.T. Leigh. To teach art, she opened a studio in Victoria Chambers, Castlereagh Street in Sydney, while her home was at "Tulagi", 30 Kemp Saint in Tennyson Point, a suburb of Sydney, where she died shortly before turning 92.
Her work was exhibited with the Royal Art Society between 1894 and 1901, consisting of wildflower studies and still-life paintings.
In 1895 her watercolour of waratahs was purchased by the Art Gallery of New South Wales. She started work at the National Herbarium of the Royal Botanic Gardens, Sydney on 3 June 1901 at the rate of "2 shillings per hour" and was earning £330 per annum at her retirement.
Foreign 27 years, from age 40 to 67, she turned out botanical drawings of the highest quality, making use of a camera lucida. There are some 1000 of her illustrations in The Botanic Gardens Trust Archive.
Consequently, she spent 12½ hours a week at the Botanic Gardens and 25 hours at the Forestry Department.
In the end Flockton stayed on at the Botanic Gardens for five years beyond her retirement age, her last day of work at the Gardens being on 24 March 1927. The lion"s share of Flockton"s work consisted of botanical illustration and she produced the necessary lithographs herself, being at that time the only female lithographer in Australia. She published various books on her own, such as a small volume "Lichens", "Australian Wildflowers" (1908), illustrated with her coloured lithographs, and produced the wildflower borders for butterfly studies in "Scenic Gems of Australia", by Doctor Riches.
Much later in life she wrote and illustrated "Children"s Stories - Little Stories of Little People", describing the life-history of plants and insects, but which remained unpublished.
One of the students in her oil and watercolour classes, was Mary Maiden, daughter of Joseph Henry Maiden. Mary later worked at the Botanic Gardens as an illustrator in a voluntary capacity.
After her retirement the vacant post was not filled until the early 1980s, when the "Flora of New South Wales" was launched, employing 19 illustrators, 16 of whom were women. The Margaret Flockton Botanical Art Award was created in her memory, and two prizes of A$5000 and A$2000 are awarded annually for excellence in botanical illustration.