The Grand harbour or Valletta is the principal seaport of Malta handling 85 % of its maritime trade. Situated on its southeastern coastline, it is a natural deepwater harbour protected by two main breakwaters. It has facilities offering ship repair and maintenance, drydocking, transhipment and storage.

Maritime activity centres on the 2 main Maltese ports, Valletta and Marsaxlokk, although a number of other ports occasionally host ships on international voyages, usually passenger vessels.

Malta Freeport (Maltese: Il-Port Ħieles) is an international port on the island of Malta with a trade volume of 3.06 million TEUs in 2015. Malta Freeport is one of busiest ports in Europe. The port is situated in Birżebbuġa in the southeastern part of Malta, on the site of the former seaplane base RAF Kalafrana.

Malta is well served with harbours, the main international ports being the Valletta Grand Harbour and the Port of Marsaxlokk. The second largest island is Gozo which can be reached from Malta by ferry from the ports of Ċirkewwa and Marsamxett or by seaplane from the port of Valletta. Gozo has one port – Mgarr.

Malta has a rich maritime heritage, and principal ports include: Malta Freeport at Marsaxlokk Harbour is the nation's principal cargo port. Grand Harbour at Valletta is a cargo port that has been in operation since the times of the Roman Empire. Marsamxett Harbour has pleasure boat marinas.