The Muscoot River is a short tributary of the Croton River in Putnam and Westchester counties in the state of New York. Approximately 6 mi (9.7 km) long and running north-to-south, it lies within the Croton River watershed and is part of the New York City water supply system's Croton Watershed.

The rivers headwaters flow southwards from gates at Kirk Lake, a controlled lake in the New York City water supply system, and Lake Mahopac, lying near one-another in the Putnam County hamlet of Mahopac, New York in the Town of Carmel. About two miles south the flow of Secor Brook joins in, an outfall from Lake Secor to the northwest. After trending slightly southeast for a bit over three miles the Muscoot drains into the Amawalk Reservoir in the town of Somers, crossing about midway along its length into Westchester County.

Upon leaving the Amawalk Reservoir via a spillway in the Amawalk Dam at the reservoir's southern end, the Muscoot is shortly joined by Hallocks Mill Brook from the west. Less than two miles later it flows into the northwestern reaches of the Muscoot Reservoir west of Whitehall Corners and northwest of Katonah, New York. The waters of Muscoot Reservoir then join with those of the New Croton Reservoir before either being carried to New York City via the New Croton Aqueduct or, in times of surplus, over the spillway at the New Croton Dam and into the Croton River, then carried into the Hudson River at Croton-on-Hudson at Croton Point about 30 miles (50 km) north of New York City.

• List of rivers of New York

41°16′10″N 73°43′31″W / 41.2695°N 73.7254°W / 41.2695; -73.7254