Initially, William's elder brother Robert was intended to take over his father's business, but when Robert opted for a military career, William began to assist his father, surveying land for the Eau Brink Cut, on the River Great Ouse, in 1797.[2] He also undertook work on the Gloucester and Berkeley Canal.[2]
In 1804, Mylne was employed by the New River Company as assistant to his father, and upon his father's retirement in November 1810,[3] he became chief engineer of the Company, a post he held until 1861.[2] From 1819 he was engaged in laying out residential streets on the New River Company's property at New River Head in Clerkenwell, including Myddelton Square, Amwell Street, Inglebert Street, and River Street.[2] Mylne later designed the gothicSt Mark's Church, Myddelton Square (1826–1828), and Clerkenwell Parochial Charity Schools (1828).[2]
Mylne married Mary Smith, the daughter of George Coxhead, and had three sons and three daughters. One son, Robert William Mylne, FRS (1817–1890) also became an architect and geologist.