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Catholic Academy of Waterbury shares Blessed Sacrament Church, which is on campus, and the Basilica of the Immaculate Conception Church, located in downtown Waterbury. Mass is held weekly throughout the school year.

Each day at Catholic Academy of Waterbury begins and ends with prayer. The day ends with a Daily Examen prayer. The Examen prayer is a technique of prayerful reflection on the events of the day in order to detect God's presence and discern his direction for us. Religion is taught as a subject in each grade level.