The Peconic River is a river within Suffolk County on Long Island, New York. The river is located in the eastern end of Long Island. The Peconic River drains an area between the Harbor Hill Moraine and flows into Flanders Bay, which in turn connects to Peconic Bay east of Riverhead. The river originates in bogs and wetlands in central Long Island near the Brookhaven National Laboratory and flows eastward to the Peconic Bay.