Cold Spring Harbor is a hamlet and census-designated place (CDP) in the Town of Huntington, in Suffolk County, on the North Shore of Long Island in New York.

Its economy mainly tied to milling and port activities, it rose in prominence as a whaling community in the mid-nineteenth century.

In the 20th century it became known as the site of Cold Spring Harbor Laboratory, although the laboratory itself is located in the adjacent village of Laurel Hollow in Nassau County, which was called Cold Spring before incorporation.

Today it is primarily a bedroom community of New York City, with a small central business area running along Route 25A, and is home to many educational and cultural organizations: the Cold Spring Harbor Whaling Museum, the Cold Spring Harbor Fish Hatchery and Aquarium (also in Laurel Hollow), Dolan DNA Learning Center, the Uplands Farm Sanctuary (home of The Nature Conservancy's Long Island chapter), and a museum exhibition gallery run by Preservation Long Island.

Cold Spring Harbor is primarily served by the Cold Spring Harbor School District, and in parts by the Huntington Union Free School District.