Ebenezer was the ninth child of John Waymouth and Eliza (nee Glanville).   He was educated at Plymouth and Cambridge (senior wrangler) and joined the Royal Navy as an assistant clerk when aged 19 in 1854 (at the time of the Crimean War). In 1859 he was promoted from clerk to Assistant Paymaster and he left the Navy in 1863.
In 1865, Ebenezer emigrated to New Zealand, as his elder brother, John, had done in 1859.   He was for 13 years the secretary and local manager of the Union Sash and Door Company.   For a while he was a general gum merchant, later becoming a public accountant and general agent.   He was a member of the Parnell Road Board and, during 1884, a member of the Parnell Borough Council.   He advocated the extension of the tramways to Parnell.
In 1870, Ebenezer married Elizabeth Mullens and they had five children - Esther Louisa (1871), Adolphus Glanville (1874), Harry Percy 1875), Claude Francis Champion (1877) and Norman Bernard de Kuyper Waymouth (1881).