[3] Sylvanus Thayer, later famous as Superintendent of West Point, was in charge of the fort's construction.

[4] In 1846 the government acquired the remainder of the island, and construction soon began on a stone fort under the Third System of fortifications.

[6] Sylvanus Thayer returned to supervise the early years of the citadel's construction, followed by Joseph K. F.

[1] Work was halted on these in 1875 and the fort was in caretaker status with only an Ordnance Sergeant for maintenance until the Spanish–American War in 1898.

Stonework from Fort Winthrop was used to build the foundation of Storrow Drive in Boston.