Under the director, there is one deputy director who assists the director with office affairs, and a chief engineer in charge of engineering and technical matters under the director's orders. There are also four divisions each with a division head: engineering, management, finance, and general affairs, and four offices: human resources, accounting, counseling and information, each with a director who carries out various business under the orders of the director and the guidance of the deputy director.

In order to promote operation and management, the Zhuoshui Creek system established Changhua Water Control Center, the Wuxi system set up the First Waterway Workstation to coordinate the allocation of water sources, and 28 irrigation workstations are responsible for irrigation management and facility maintenance.