The Aqueduct was built between 1839 and 1841 as part of the Enlarged Erie Canal, was perhaps the single greatest improvement made during the canal's enlargement phase. The 14 arch, 624-foot long aqueduct carried the Enlarged Erie above and totally apart from the Schoharie Creek.

Because the original 1820's Erie Canal entered the creek itself, whenever the Schoharie was flooding, traffic on the canal was often halted for days. After the aqueduct went into operation, canal traffic no longer had to be interrupted. The aqueduct was abandoned in 1917, when the barge canal opened in the Mohawk River. It remained intact until the late 1930's or early 1940's, when two of the arches at its east end collapsed. Three or more arches were removed subsequently to allow for the ice jams to flow out of the Schoharie Creek.

The Schoharie Aqueduct was built by a Schenectady contractor by the name of Otis Eddy at a cost of $180,000.