W. Wardlaw Thompson received his schooling at the South African College, Cape Town, from 1858 to 1863. He entered the civil service of the Cape Colony in 1877 as a temporary clerk in the Railway Department. In January 1878 he was appointed as a clerk in the Public Works Department, rising to first clerk in November 1882. He was transferred to the Crown Lands Office as chief records clerk in January 1885, promoted to first class clerk in the Department of Agriculture in July 1889, and as acting chief clerk in the same department in November 1897. At some time before 1896 he passed the civil service law examinations. He was on active service with the Duke of Edinburgh's Own Volunteer Rifles in the Transkei (February to May 1879) and in Basutoland (now Lesotho, September 1880 to March 1881). In October 1897 he became a member of the Fisheries Board.
Thompson left his clerical post in 1905 to become the assistant of John D.F. Gilchrist*, government biologist of the Cape Colony and honorary curator of marine invertebrates at the South African Museum. Over a period of ten years he contributed to several important publications, each time as Gilchrist's co-author. By 1907 they had completed a study of the local Klip fishes (Family Blenniidae), based on a large collection procured chiefly at the South African Museum's aquarium at St James, Cape Town. This work was published as "The Blenniidae of South Africa" in the Annals of the South African Museum (1908, Vol. 6, Part 2). Two years later they presented a paper on "The Cape Klipfishes" at the annual congress of the South African Association for the Advancement of Science (Report, 1910, pp. 214-225).
By 1907 Gilchrist and Thompson were also busy drawing up a descriptive catalogue of the sea fishes of Natal. It was published as "Descriptions of fishes from the Natal coast", in four parts, in the Annals of the South African Museum (1908-1914, Vol. 6, Parts 2 and 3; Vol. 11, Part 2; Vol. 13, Part 3), totaling some 190 pages. Their descriptions were also published in the Annals of the Durban Museum (1914-1917, Vol. 1, pp. 255-431) under the title "A catalogue of the sea fishes recorded from Natal". They also described four new South African fishes in Gilchrist's Marine Biological Report (No. 3) for 1916.
Gilchrist and Thompson were the first local scientists to study the freshwater fishes of South Africa and to compile a comprehensive catalogue. They described three new species in the Annals and Magazine of Natural History in 1911, while their catalogue, which included some 200 engravings, was published in three parts in the Annals of the South African Museum (1913-1918, Vol. 11, Parts 5, 6 and 7).
On his own Thompson wrote a book on The sea fisheries of the Cape Colony from Van Riebeeck's days to the eve of the Union (Cape Town, 1913). It included chapters on the whale and seal fisheries, trout and other freshwater fishes, and oysters. Thompson was a Fellow of both the Linnean Society (FLS) and the Zoological Society of London (FZS). In 1902 he became a foundation member of the South African Association for the Advancement of Science and by 1910 was a member of the Royal Society of South Africa.
