Owing to its position on the East Coast of England, the yard was of strategic importance during the Anglo-Dutch Wars; however, due to a lack of deep-water access and the difficulty of setting off from Harwich against an easterly wind, its usefulness was somewhat limited and its facilities remained small-scale compared to the other Royal Dockyards over the same period.

[2] After the Royal Navy withdrew from the yard in 1713, shipbuilding continued on the site under private ownership; over the course of the next century, through to the end of the Napoleonic Wars, just under forty more warships were built there.

[2] The present-day name for the site of the former Dockyard is 'Harwich Navyard';[1] for the past 50 years it has been run as a commercial port, however in 2018 plans were announced for it to be transformed into space for more than 300 homes.

[1] In 1664, however, the yard was taken back under Crown control: a new resident Commissioner (John Taylor) was appointed and Samuel Pepys, as Clerk of the Acts of the Navy, engaged his protégé Anthony Deane as Master Shipwright.

Not only was it kept busy repairing and refitting naval vessels on their way to and from the front line, but under Deane's skilled oversight it also began to be active in shipbuilding.

[5] In 1676, Silas Taylor (the aforementioned 'Keeper of the King's Stores at Harwich') wrote a description of the dockyard: it had wharves, built on reclaimed land, with strong cranes (one of which had been rendered unusable by the action of the tide depositing sand against the wharf).

[8] One unusual structure surviving from the dockyard is a very rare treadwheel crane of 1667, which was in use until the early twentieth century before being re-sited on Harwich Green in the 1930s.