John was the eldest of six children of John Waymouth (Cooper John) and Mary (nee Penn) of Millbrook, Maker, Cornwall.   He served his apprenticeship as a shipwright at the Devonport Dockyards and married Eliza Glanville (see) at Rame on 1 August 1820.   Soon after the marriage, the couple moved to Pembroke, Wales where John was employed at Pembroke Dock.   Their first eleven children were born there between 1821 and 1839, the last being born at Devonport in 1843.
At Pembroke, John rose to be Inspector of Shipwrights and at Devonport he was promoted to the rank of Timber Inspector (hence the name Timber John).   Sometime after the reopening of Deptford Dockyard on the Thames in 1844, John was promoted to Foreman of Shipwrights there.   He was back at Devonport in 1860 when he wrote his will and stated that he was Foreman of the Yard.