Waterhouse was born the third child of seven at Chatham Kent on 22 January 1883, his father being a shipbroker. He was educated at Bancroft's School in 1894-1900 and then at the University of London. At the time of the UK 1901 national census, the family were living in East London, where Gilbert's occupation, aged 18, was given as a ship's Draughtsman. He later qualified as an architect (RIBA) and gave his profession as "architect-surveyor" when he enlisted in the army on 8 September 1914.