The Underwater Archaeology Collection of the Archaeological Museum of Istria was founded in 2015 with the aim of researching, protecting, and valorising underwater archaeological sites in the Istrian area. 

The history of the first underwater research in Istria dates back to 1963 when, on the initiative of archaeologist Štefan Mlakar, a curator at the Archaeological Museum of Istria, the remains of a shipwreck with a cargo of wine amphorae from the 1st century BC were explored near Cape Savudrija. 

With the development of autonomous diving, military and civilian divers began to gather around Mlakar from the mid-1960s, participating in organised searches of the Istrian seabed. Although Mlakar himself was not a diver, he was in charge of conducting underwater surveys to collect archaeological finds and data on underwater sites in Istria. These searches were carried out until the mid-1970s, after which a long pause followed. 

The Museum became actively involved again in 2007, conducting rescue excavations of a submerged Roman villa near Pomer. In 2011, it began a multi-year international collaboration with the universities of Salento and Trieste to research the Roman port in Savudrija, one of the most important ports in the northern Adriatic. It also conducts research on prehistoric sites in Zambratija Bay, including Eneolithic pile dwellings, a project which the University of Bern joined in 2023, and a Bronze Age sewn boat, which is the oldest vessel made using the sewing technique in the Mediterranean. A long-standing collaboration with the French Centre Camille Jullian (CNRS) has resulted in both the research and the recovery of the boat in Zambratija, and prior to that, two Roman sewn boats in Pula. The discovery of ancient sewn boats testifies to the highly developed technological level of shipbuilding in the Istrian area, and thus the importance of seafaring, which points to the significance of navigation along the northern Adriatic coast.

The Museum also systematically conducts research on the Roman salt pan in Bijeca Bay near Medulin, currently the only confirmed one on the Istrian coast, as well as work on numerous other underwater sites.

Successful cooperation with clubs and associations of the Diving Federation of the Istrian County contributes to the research, preservation, and promotion of underwater archaeological heritage.