The museum's origins lie in the former Board of Submarine Archaeological Excavations of Cartagena, created in 1970 and associated in 1973 with the Submarine Archaeology Centre of Cartagena. Finally, the National Museum of Maritime Archaeology and National Centre for Submarine Archaeological Research was created in 1980, and officially opened in 1982.
This marked the beginning of an intense programme of systematic prospecting on the coast, as well as professional diving and underwater archaeology courses. The Laboratory for Water-Saturated Archaeological Wood was also created, and publication began of the Monographic Catalogues of the museum's holdings and the journal 'Cuadernos de Arqueología Marítima'.
Notable finds included the Phoenician shipwrecks of the Playa de la Isla de Mazarrón.
The museum has gained an international profile, from the 1997 Euro-Mediterranean Forum for Underwater Archaeological Heritage (FEMAM) to its current projects: Archeomed, studying and restoring the maritime cultural heritage of the Mediterranean; the Maritime Archaeological Heritage Route in Spain and Portugal; the Network of Museums and Institutes for Research and Protection of the Marine Cultural Heritage of the Mediterranean (Sicily POR 2000-2006); and the MEDMUS Museum Network (Museums in the Mediterranean Region).
Its most important archaeological interventions since 2007 are: archaeogeophysical prospecting in the bay of Cartagena, in collaboration with the Aurora Trust Foundation; collaboration with INA in the project Bajo de La Campana; and conservation and protection in situ on the site of the Phoenician boat Mazarron 2.
In 1992, the Cartagena Port Works Board, now the Port Authority, fulfilling general guidelines of the Ministry of Development for all State Ports, decides to dismantle the sheds of the port and return those lands to the City, which had been deprived of direct access to the sea since those lands were won to the water to the end of the s. XIX.
In the enormous extension, the Port Works Council decides to donate a parcel to the Ministry of Culture for the construction of a new headquarters for the Museum-Center.
This was an imperative need since the current headquarters had deficiencies such as lack of space for basic functions, or storage and exhibition of objects, as well as spaces needed for a Museum as a temporary exhibition room or activities Didactics. The center also suffered a great lack of personnel.
Thus, during 1994 and 1995, the offering of lots of the Board of Works of the Port, that contemplated a Museum of 2,800 m² was formed.
In this way and as an immediate result, in 1995 a preliminary project was commissioned on 6,000 m2 for the new Museum to the architect Guillermo Vázquez Consuegra, being Minister Carmen Alborch.
The following year, in May 1996, this preliminary draft was officially presented at the Palacio de San Esteban (Murcia), the Seat of the Presidency of the Region and finally, in 1999, the Ministry took the project to public competition, after which was awarded to the construction company "Fomento de Construcciones y Contratas".
The works began in January 2001. And finally, on January 23, 2002, after six years of negotiations, the first stone was laid.
Due to several problems, the initial project of the building was reduced in extension, and thus, fundamentally, it is necessary to speak of: The loss in meters, by drastic reduction of the surface of the building of the Center, of 6000 to 3800 m². The loss in height, until the highest part of the Carlos III wall, located behind the lot. The loss of the well and the test pool as well as the Temporary Exhibition Hall.
Finally, the new headquarters of the Museum was inaugurated in 2008 in the Paseo del Muelle Alfonso XII.
In 2014 the Museum inaugurated in its Permanent exhibition "Ocean Navigation", a new part of it that houses the cargo of the Frigate Our Lady of the Mercedes, of which the Museum is depository. In addition, the Museum's laboratories were also created in 2012, in an external building, the main headquarters, in a large industrial building on the outskirts of Cartagena.
In addition, the Museum is currently developing several research routes, among which, due to its international importance, are the campaigns on the Pecio Nuestra Señora de las Mercedes (2015 and 2016), projects for the restoration of organic and inorganic materials, as well as research on other Spanish deposits in national non-territorial waters.