Fort Wellington was established at Prescott during the War of 1812 to protect a vulnerable section of the St Lawrence River. The waterway carried supplies between Montreal and Kingston, making control of its banks important to British military operations in Upper Canada. Across the river stood Ogdensburg in the United States, so the frontier was immediate and visible. Construction began in 1812 and continued as the conflict developed. The original fort belonged to a wider system of posts intended to secure transport rather than defend one town alone.

In February 1813, British forces under George Macdonell crossed from Prescott and attacked Ogdensburg, disrupting American operations along this stretch of the border. The action illustrates the offensive as well as defensive role of the garrison. After the war, military attention fluctuated and the first fort deteriorated. Its later rebuilding followed a new crisis: the rebellions of 1837 and subsequent cross border activity by sympathisers seeking to overthrow colonial government. These events renewed concern about the river corridor and the security of settlements close to the United States.

The present fort largely reflects construction in 1838 and 1839. A substantial stone blockhouse formed its core, enclosed by earthworks and a palisade. Defensive features, storage and accommodation were combined within a compact installation. The nearby Battle of the Windmill in November 1838 demonstrated the threat posed by armed incursions, although that battlefield is a separate place. Fort Wellington's design and rebuilding therefore belong primarily to this later emergency, and should not be attributed wholesale to the opening years of the War of 1812.

During the 1840s, soldiers of the Royal Canadian Rifle Regiment occupied the fort, and family life became an important part of the garrison's story. Married soldiers, women and children shared an environment also organised around drills, guard duty, supplies and discipline. Later tensions, including the Fenian threat in the 1860s, briefly renewed its military relevance. As strategic needs changed, the fort lost its active defensive role. Its survival depended increasingly on recognition of historical value rather than the usefulness of its walls against modern weapons and tactics.

Fort Wellington received national historic recognition in 1920 and is preserved as a Parks Canada site. Interpretation often focuses on the mid nineteenth century garrison, allowing domestic arrangements and military routines to be considered together. Exhibits also place the fort within the broader history of river transport and defence. Its significance rests on the relationship between the St Lawrence supply route, a contested border and the people stationed beside it. The surviving blockhouse and earthworks make those connections tangible while preserving evidence of a fort repeatedly adapted to changing emergencies.