Windham High Peak stands within the watershed of the Hudson River, which drains into New York Bay.
The south and northwest sides of Windham drain into Batavia Kill, and thence into Schoharie Creek, the Mohawk River, and the Hudson River.
The northeast side of Windham drains into Bowery Creek, thence into Catskill Creek, and the Hudson River more directly. And the southeast side drains via Plattekill Creek into Esopus Creek, a still lower Hudson tributary. The summit trijunction of the divides between these watersheds demarcated, until at least 1629, the traditional boundary tripoint of Mohawk, Mohican, and Delaware territory, respectively.