William was the eldest of three sons of William Waymouth (architect) and Catherine (Dubberley, nee Omer).
William's father was a builder, surveyor and then architect.   It is not surprising that William John was a builder's clerk when he married at the age of 19 in 1857.   He married his first cousin, Eliza Waymouth.   Eliza (see) was a daughter of John Waymouth (timber John) and Eliza (nee Glanville).   They had one child, Eliza Catherine Waymouth, named after her two Waymouth grandmothers.   Sadly, the daughter, Eliza, died in 1870 at the age of twelve years.   John Blackman, a relation by marriage, wrote an elegy in memory of "Kate".
In 1881, William and his wife, Eliza, were living at Islington.   William was a Senior clerk at the Admiralty in Whitehall.
Eliza died in 1895 and in 1901, William was retired and living in St Helens, Hastings, Sussex.   In the same house was a cousin, Susan Edith Waymouth, a daughter of Henry Waymouth, a brother of William's late wife.