Indian Point draws up to 2.5 billion gallons of water a day from the Hudson River to cool its two nuclear units.
The DEC says Entergy's proposed 20-year continued operation "would continue to exacerbate" the harm done to fish, fish eggs and larvae.
There was no immediate comment from Entergy which could request a hearing, challenge the decision or seek an extension from the Nuclear Regulatory Commission.
The power plants are located about 35 miles north of Manhattan.