The museum was founded in 1953, based on the private collection of its founder and first director, Aryeh Ben- Eli. In 1972, the museum moved to its current premises near the northern beachhead of Mount Carmel, between Stella Maris and Bat Galim neighborhoods. Nearby are the Israeli Clandestine Immigration and Naval Museum and the Cave of Elijah.
The Marine Workshop of the Leon Recanati Institute for Maritime Studies, affiliated with the University of Haifa is located at the museum. The workshop provides professional diving and field surveying services for field research conducted at the institute.
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