Frederick Stephanus Watermeyer was a son of Godfried A. Watermeyer, a brother of the chemist James Charles Watermeyer*, and a grandson of the well-known Cape Town businessman Frederick Stephanus Watermeyer* senior. Frederick Stephanus junior was awarded the third-class certificate in literature and science of the Board of Public Examiners of the Cape Colony (more or less equivalent to matric) in 1870. He then qualified as a land surveyor and was admitted to practice in the Cape Colony in July 1873. In 1881 he was admitted to practice also in Natal. He appears to have worked in the South African Republic (Transvaal) from 1889, and is known to have surveyed the suburb Goede Hoop in Pretoria in 1897. After the Anglo-Boer War (1899-1902) he was admitted to practice in the Transvaal Colony on 11 July 1902. In 1904 he was elected vice-president of the Institute of Land Surveyors of the Transvaal. After holding this position to 1908 he was elected president of the Institute for 1908/9.
On 29 August 1905, at a joint meeting of the British and South African Associations for the Advancement of Science in Johannesburg, Watermeyer read a paper entitled "Geographical notes on South Africa south of the Limpopo". He summarised the history of the country's cartography, sketched the history and distribution of its indigenous population and European colonists, discussed the physical features and climate of the region and their effect on agriculture, and provided a table of all the principal South African towns with their latitudes, longitudes, heights above sea level and annual rainfall. The paper was included in the Addresses and papers... published after the meeting (Vol. 1, pp. 293-318) and was also published in the Journal of the Institute of Land Surveyors of the Transvaal (1905, Vol. 1(2), pp. 15-35) and in the Scottish Geographical Magazine (1905-1906).
Watermeyer was listed as a government surveyor in Pretoria to at least 1916, and remained there until his death in 1919. He became a member of the British Association for the Advancement of Science in 1905. In 1906 he also joined the South African Association for the Advancement of Science, and was still a member in 1918. He was married to Mary Ethel Hill, who died in May 1908, and was survived by two daughters and a son. His biographical details can easily be confused with those of other persons with the same names.