[3] Pemaquid has a colonial settlement history dating to the early decades of the 17th century, with a succession of conflicts leading the site to be attacked on several occasions and entirely abandoned twice.

King Philip's War, a major conflict that engulfed New England in 1675, resulted in attacks on Pemaquid and its outlying settlements, and the community was abandoned in 1676.

New York authorities reasserted control over the area after the war, and established a formal administration, granting monopoly trading rights to a few favored residents.

The Dominion governor Edmund Andros built a wooden fort in 1688, which did not prevent the community from being sacked at the outbreak of King William's War in 1689 by a combined force of French and Indians.

[3] In 1729 David Dunbar, a local crown representative and entrepreneur, sought to establish an colony of Irish settlers called "Georgia" at Pemaquid, and constructed Fort Frederick.

Massachusetts political leaders opposed this attempt to establish another colony, and successfully petitioned the king to regain control of the area.

Fort Frederick was demolished by local authorities during the American Revolutionary War to prevent its use by British troops, and the area became a rural backwater.