Marsascala was inhabited thousands of years ago according to various remains found in the area.  Roman era villas, Roman Baths, as well as early Christian catacombs found in the town suggest that Marsaskala once was a Roman port. The parallel channels formed in the rock face called cart-ruts, and they are certainly some of the oldest remains. Some of them unexplainably lead straight into the sea. It is still not sure how they were made or what was their purpose.

During the time of the Knights in 1614 a 60-strong fleet of Turkish ships carrying around 600 solders made a surprise attack on Marsascala. However the Maltese gave them a hard battle, and finally drove the Turkish soldiers away. After this attack fear, and memories of the 1565 Great Siege of Malta was brought back, and Grandmaster Alof de Wignacourt decided that improved fortifications were necessary in this sensitive area. In the same year St Thomas tower was build and finished by the Knights of St John. The huge fortress takes its name from St Thomas Church nearby.