St Thomas' Bay is a bay in southeastern Malta, located in the limits of the seaside town of Marsascala.

Marsaskala, also written as Marsascala and abbreviated as M'Skala, is a seaside town in the South Eastern Region of Malta which has grown around the small harbour at the head of Marsaskala Bay, a long, narrow inlet also known as Marsaskala Creek. The bay is sheltered to the north by Ras iż-Żonqor, the southeast corner of Malta, and to the south by the headland of Ras il-Gżira. The parish church, built in 1953, is dedicated to Saint Anne and the feast is celebrated at the end of July in Marsaskala.