The first military installation on this site was an earthwork fort (redoubt) with four "great guns" erected in 1632. This early fort was followed by a timber blockhouse built in 1666. By the time William and Mary came to the throne of England, a strong rivalry with France had developed and stronger defenses were required. Cannon and military stores were sent from England in 1692 and a breastwork was constructed to protect them. This fort was named Fort William and Mary and took its place in the line of so-called castles along the coastal area of the colonies. Although additional guns were sent and repairs were made to the fort from time to time during the French and Indian Wars, the breastwork remained essentially the same until the time of the Revolution. Each breastwork was a rampart of turf three feet high on which batteries of guns were clamped to wooden platforms protected by a stone wall about seven feet high. The stone walls had window-like openings called embrasures through which the guns were fired.

It was on the eve of the Revolution that the fort played its most dramatic role in history. On December 13, 1774, Paul Revere rode from Boston with a message that the fort at Rhode Island had been dismantled and troops were coming to take over Fort William and Mary. The following day the drums beat to collect the Sons of Liberty, and 400 men from Portsmouth, Rye and New Castle raided the fort and removed 98 barrels (approximately five tons) of gun powder.

The next night, a small party led by John Sullivan carried off 16 pieces of small cannon and military stores. This raid took place months before the incidents at Concord and Lexington, and was an important event in the chain of events leading to the Revolution. Governor John Wentworth immediately sent to Boston for help. The sloop Canceaux arrived December 17, followed two days later by the frigate Scarborough. The latter had 40 guns and carried 100 British marines on board. This prevented further raids by the patriots, but produced a dangerous state of tension.

By the summer of 1775, Governor Wentworth, with Lady Frances and their infant son, took refuge in the fort and lived there two months in hopes that a conflict could be avoided. Admiral Graves sent a transport under the Falcon to dismantle the fort and carry off the cannon to Boston. Finally on August 24, 1775, the Governor and his family sailed to Boston on the Scarborough. Wentworth made a brief visit a month later when, from the Isles of Shoals, he issued a proclamation discontinuing the assembly. This was the last act of royal authority in New Hampshire.