The museum holds about 6,000 documents and artifacts from Cold Spring Harbor and other Long Island whaling towns.

The library and archival collection contains 2,800 primary and secondary volumes and manuscript material from the Cold Spring whaling fleet, ship’s logs, journals and business correspondence of the Cold Spring Whaling Company, family documents dealing with maritime commerce on Long Island, records of the Long Island coastwise trade under sail and records from the Cold Spring Harbor Customs House (1798 until 1908).

Totaling 6,000 pieces, most pieces speak to the 19th century whaling industry, specifically Long Island whaling, as well as the local history of Cold Spring Harbor and its growth as a maritime port.

The collection includes:[2] In 1932, a small number of residents of Cold Spring Harbor, New York, commissioned a monument commemorating the village's earlier days as a whaling port.

A boulder was dredged from the harbor and erected on the village square and lists the names of the nine vessels in the fleet.