Indian Point 3 was manually shut down after control room operators observed fluctuating water levels inside a steam generator.
Operators say that one of the unit's condensation pumps malfunctioned. The pump feeds water to the system's steam generators.
This was the third time in three weeks that the nuclear reactor was taken offline.
It is one of the main reactors that supplies power to New York City and Westchester.
Entergy officials say there is no public threat and no radiation was released as a result of the shutdown. A spokesperson says all equipment at the nuclear power plant operated as expected.
The plant's other reactor is operating at full power, keeping Indian Point running. There is no word on when reactor 3 will be back online.
Reactor 3 is the same unit where the main transformer exploded and caught fire back in May, sending thousands of gallons of oil into the Hudson. Just last month, the same unit was shut down again when a balloon got tangled in electrical wires at the plant.