This paper describes the design and implementation of a real-time flow control system on a major trunk sanitary and relief tunnel system in the City of Ottawa. The flow control system was designed to provide added protection against basement flooding, prevent sanitary sewer overflows (SSOs) and to provide for optimized system operation under both existing and future flow conditions. The flow control system consists of a modulating gate-actuator assembly tied to the City’s SCADA system, which acts as both a flow monitoring and flow control system. The flow control system is designed for optimum system operation by maximizing the amount of flow conveyed along the main trunk sewer system and minimizing the frequency of diversions to the Tunnel relief system where pumping is required to convey flows to the Wastewater Pollution Control Plant.