William Whitaker studied at University College, London, where he was awarded the Bachelor of Arts (BA) degree in chemistry in 1855. Two years later he joined the Geological Survey of Great Britain as an assistant geologist. He was promoted to geologist in 1863 and to district geological surveyor in 1882. Most of his work involved geological surveying and mapping in south-eastern England and led to the publication of around 100 reports, papers and explanations of geological maps between 1861 and 1903. A number of his reports dealt with the water supply of various regions. In 1867 he published an original and carefully researched paper on subaerial denudation which finally ended the belief that escarpments were formed only by marine erosion. His most important geological mapping centred on London and the Thames valley, leading to major publications on the geology of the London basin in 1872 and 1889. He also compiled several outstanding bibliographies on the geology of different English counties.
Whitaker visited the Cape Colony in or before 1866, but did not publish anything on its geology. He did, however, collect stone artefacts. Some of these were presented to the Pitt Rivers Museum, Oxford, in 1866, and some more to the British Natural History Museum in 1867.
Whitaker retired from the Geological Survey in 1896 and settled in Croydon, just south of London, as a water engineer. He has been described as the "father of English hydrogeology" (Oxford dictionary of national biography, 2004) He became a member of the British Association for the Advancement of Science in 1859, served on its council from 1890 to 1896, and as president of Section C in 1895; was elected a Fellow of the Geological Society in 1859, served as its president from 1898 to 1900, and was awarded its Murchison medal in 1886, its Prestwich medal in 1906, and its Wollaston medal in 1923; was elected a Fellow of the Royal Society of London in 1887 and served on its council during 1907-1909; was president of the Geologists' Association for 1900-1902 and 1920-1922; and was active in many other scientific societies. He has been described as a kind, good-tempered and honest gentleman.