Harwich had been a naval gathering point long before there was a permanent yard. In June 1340, during the Hundred Years' War, King Edward III sailed from the mouth of the Orwell estuary with 200 ships to fight the French fleet off the Flanders coast. The resulting Battle of Sluys was an English victory and one of the most decisive sea battles of the medieval period. In 1405, during the reign of Henry IV, a fort was built on the promontory at the north-eastern point of Harwich to defend the anchorage; it would later evolve through several rebuildings into Landguard's sister fort across the estuary. Through the Tudor period the fort fell into disrepair but the natural harbour kept its strategic importance: the rivers Stour and Orwell empty into a deep, well-protected anchorage facing the Low Countries, an obvious base for any war on the eastern approaches.

During the Commonwealth period the government took a 99-year lease on the parcel of land where the old fort had stood, and began establishing a naval dockyard. In 1664, the year before the Second Anglo-Dutch War broke out, the Crown resumed direct control. A new resident Commissioner, John Taylor, was appointed; Samuel Pepys - then Clerk of the Acts of the Navy and the figure who modernised English naval administration - engaged his young protege Anthony Deane as Master Shipwright. Deane was one of the great shipbuilders of his generation. Under his supervision Harwich Dockyard developed a specialty in small and medium-sized fighting ships: nimble vessels suited to the shallow North Sea, well below the great hundred-gun ships built at Chatham or Portsmouth. During the Second Dutch War the yard repaired and refitted vessels coming off the front line and laid down new keels. In the Third Dutch War, between 1673 and 1675, Deane - by then a Commissioner of the Navy - built three more warships at Harwich as a private contractor. One, HMS Harwich, was considered by Pepys himself to be one of the finest ships in the Navy.

In 1676 the storekeeper Silas Taylor, who had held the role since 1664, wrote a description of the yard. It had wharves built on reclaimed land, with cranes - one disabled by the slow tidal deposit of sand against the wall. A 'Great Gate' bore the Royal Arms in carved and painted relief; over the gate, inside and out, were the dials of what Taylor called an 'excellent' pendulum clock that struck the hours on a bell housed in a small turret. The same bell, rung at the beginning and end of the working day, served as a muster bell for the workforce. Inside the yard were storehouses for timber, rope, canvas, and ordnance; launches - what we now call slipways - for laying down and sliding ships into the river; and offices for the officers, clerks, and shipwrights. The dockyard bell from 1666 still survives on site. The treadwheel crane, built in 1667 - two wheels worked by men walking inside them, with no other source of power - lifted the heaviest cargoes and ship's components for nearly two hundred and fifty years. It was in use into the early twentieth century before being re-sited on Harwich Green in the 1930s.

Harwich's strategic value depended on its facing the Dutch coast. Once the Anglo-Dutch Wars subsided and English naval attention shifted, the yard lost its central role. Its limitations were real: shallow water on the approaches, and an easterly wind out of the North Sea that often made it difficult to put ships to sea. By the Third Dutch War, the navy's main east-coast dockyard had moved to Sheerness on the Thames. Harwich ceased operating as a Royal Dockyard in 1713 but was leased out under a succession of private operators - John Barnard, Messrs Barnard and Turner, Joseph Graham - who continued to build warships under contract and merchant vessels alongside them. The last Royal Navy ship built here was HMS Scarborough, launched in 1812. The last commercial vessels were ten steamers built between 1825 and 1827. After that the yard wound down. The site continued as a working port and remains so today, operating since 1964 under the name Navyard.

The yard's life as a Royal Dockyard was over, but Harwich's naval life was not. In the First World War the harbour was home to the Harwich Force, a flotilla of cruisers, destroyers and submarines under Commodore Reginald Tyrwhitt that fought across the North Sea throughout the conflict, including at the Battles of Heligoland Bight and Dogger Bank. In the Second World War parts of the port were again requisitioned for naval use. Ships were based at HMS Badger, a shore establishment on the site of what is now Harwich International Port. Badger was decommissioned in 1946. The Royal Naval Auxiliary Service maintained its headquarters there until 1992, when it too disbanded. Today the dockyard's most visible monument is the treadwheel crane on Harwich Green - a curiosity, a working museum piece, a reminder that for half a century in the seventeenth century, ships of the line slid into the water at this small estuary.