A system and method are provided for presence based automatic operation of a marine barrier gate for protecting a secured area. Embodiments include a system having RFID sensors outside and inside the secured area, and proximal the gate. A controller verifies that a user is authorized to enter the secured area when one or more of the RFID sensors communicate with a user identification unit carried by the user; opens the gate or causes the gate to remain open when the user's authorization to enter the secured area is verified; tracks a location of the user identification unit using the RFID sensors while the gate is open and the user is transiting the gate; and closes the gate when the RFID sensors are no longer in communication with the user identification unit.