[1] 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.

It is the longest river on Long Island and is almost entirely within the Central Long Island Pine Barrens publicly protected area, which was set up in 1993 to protect its relative wilderness standing.

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