Stony Brook is a hamlet and census-designated place (CDP) in the Town of Brookhaven in Suffolk County, New York, United States, on the North Shore of Long Island.

It began as a satellite community of adjacent Setauket, New York, the Town of Brookhaven's first settlement, and its land was included in the initial 1655 purchase from the native Setalcott tribe.

For religious services and education, the hamlet's original residents had to attend institutions in the neighboring communities of Setauket and St. James.

In the latter half of the 18th century, activity began to shift from the mill area north toward the harbor as new residences, a number of which still stand, were constructed.

[3] Stony Brook was a remote area through the 18th century aside for a modest amount of commerce near the mill at the intersection of Main Street and Harbor Road.

Lacking the resources of its neighboring harbor settlements, Stony Brook based its economy on agriculture and the cordwood industry.

Stony Brook quickly became a popular summer resort for city dwellers attempting to escape the hazards and stress of urban life.

The history of the unincorporated "village" is closely linked to that of Ward Melville, a local businessman who owned what would become the CVS Corporation.

To accomplish this, Melville moved many of the existing shops in the plot into the crescent and modified their details for consistency, a design model similar to that of Colonial Williamsburg.

As a centerpiece to the crescent, Melville built the Stony Brook Post Office, decorated by a large eagle that flaps its wings to mark each hour.

Other Stony Brook attractions are the 19th-century William Sidney Mount House, the St. James Episcopal Chapel, and the West Meadow Beach Historic District.

Stony Brook is on the North Shore of Long Island, approximately 55 miles (89 km) east of the New York City borough of Manhattan.

[4] However, a small section of the hamlet's southwestern extreme is located within the boundaries of (and is thus served by) the Middle Country Central School District.

[4] The Stony Brook station of the Long Island Rail Road's Port Jefferson Branch is located within and serves the hamlet.