System Operations is responsible for operating the potable water system to ensure reliable and sustainable deliveries to District customers. To accomplish this, Water Operations utilizes a Supervisor Control and Data Acquisition (SCADA) system that controls water flow and storage through the District's distribution system. Additionally, this department performs various maintenance, monitoring, and evaluations of the District's storage reservoirs, tanks, pump stations, and chlorine booster and monitoring stations. System Operators provide routine maintenance and repairs for all pumps in the distribution system.

Water Quality is a part of System Operations. The system operators are responsible for collecting routine samples used to monitor water quality in the distribution system. This includes unique sampling for California State Water Resources Control Board requirements, contractors, and construction crews working on the District's pipelines. Other components of Water Quality include responding to water quality complaints, pipeline flushing, and the preparation of monthly, quarterly, and annual reports for the State Water Resources Control Board.

Valve Maintenance is responsible for the District's valve exercise program while maintaining all appurtenances such as fire hydrants, wharf heads, blow-offs, and air release valves. This includes the repair, replacement, painting, and upkeep of easements. Valve Maintenance ensures that distribution valves are operational and ready to isolate the water mains in emergencies, routine maintenance work, and new construction projects. Valve Maintenance also assists with shutdowns for the construction/maintenance department and contractors by operating the valves that shut down the main lines