Saint Thomas Tower was built above the shore on the seaward face of the headland of Il-Hamriga in Marsaskala. It is a substantial fortification intended to prevent the landing of troops in the sheltered anchorages of Marsaskala Creek and St Thomas Bay. The tower was built in 1614 and was named after a chapel dedicated to St Thomas which stood close to where the tower now lies. Its architect is not known and it cost 13,450 scudi to build making it the second most expensive Wignacourt tower.
The tower has very thick walls and has four pentagonal turrets projecting outwards on each corner. The tower’s entrance was through a vaulted doorway with a wooden drawbridge. The drawbridge is still partially intact and it is the only original one to have survived in Malta.
After the De Redin towers were built, St Thomas had Żonqor and Xrobb l-Għaġin Towers in its line of sight, but these are now either in ruins or completely demolished. In 1716, St Thomas Tower was reinforced by the addition of a battery on the seaward face. Construction of the battery cost a total of 382 scudi, 8 tarì, 11 grani and 1 piccolo, which was less than the cost of construction of other batteries around the coast. The tower continued to be used by the British until well into the 19th century, but unlike St Lucian Tower the battery around the fort was not dismantled and rebuilt and only minor alterations to the tower itself were made.
The tower and battery have undergone recent restoration work. The village of Marsaskala has expanded to surround the tower with modern buildings, and the tower now forms the centerpiece of a plaza around its shoreward face. The tower was used as a restaurant and pizzeria. In 2008 the tower was cleaned and the ditch was cleared of vegetation so it is now in very good condition. It was to be converted into a museum about piracy in the Mediterranean.