Blackhead stands within the watershed of the Hudson River, which drains into New York Bay.
The southwest side of Blackhead drains into East Kill, thence into Schoharie Creek, the Mohawk River, and the Hudson River.
The north side of Blackhead drains into the headwaters of Batavia Kill, and thence into Schoharie Creek.
The east side of Blackhead drains into Trout Brook, thence into Shingle Kill, Catskill Creek, and the Hudson River.