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.

1. Assist the Director in managing departmental affairs.

2. Review and finalize drafts and plan key business matters.

3. Coordinate business-related communications and oversee important assigned cases.

4. Evaluate and enhance business performance.

5. Supervise and coordinate cross-departmental activities.

6. Carry out tasks assigned by the Director.

1. Assist the Director with technical matters related to engineering and management.

2. Supervise and conduct research on water resource utilization and irrigation management.

3. Oversee the planning, design, and operation of engineering projects.

4. Review engineering plans and designs, and assess the quality and progress of construction.

5. Plan engineering budgets and oversee the bidding and tender processes.

6. Conduct research on the benefits of water resource development and irrigation projects.

7. Execute tasks assigned by the Director.

The Engineering Division is subdivided into the Design Section, Construction Surveillance Section, and Construction Section. It handles the planning, surveying, design, construction oversight, and acceptance of water conservancy facilities, including their development, improvement, and repair.

The Management Division is subdivided into the Irrigation Section, Supervision Section, Mechatronics Section, and Water Quality Section. It manages water resource development, allocation, and operations, water quality monitoring and testing, irrigation management, water conservancy facility maintenance, disaster repairs, local water conservancy teams, pump maintenance, and drought irrigation promotion.

The Finance Division is subdivided into the Expropriation Section and Property Section. It manages revenue from irrigation operations, including asset activation, revenue management, real estate management and disposal, and the preparation and adjustment of annual financial plans.

The General Affairs Division is subdivided into the Documentation Section, General Affairs Section, Cashier Section, and Contracting Section. It handles documentation, cashier operations, office management, seal control, committee meetings for the Irrigation Advisory Council, and tendering and contracting processes.

The Human Resources Office is subdivided into the Appointment and Removal Section and the Performance Evaluation Section. It oversees organizational matters, employee appointments, dismissals, compensation, benefits, evaluations, rewards and penalties, attendance, training, retirement, and related compensation matters.

The Accounting and Statistics Office is subdivided into the Budgeting Section, Accounting Section, and Statistics Section. It prepares annual budgets and final accounts, audits accounting documents, and manages statistical data.

The Counseling Office is subdivided into the First Section and Second Section. It manages public petition cases, evaluates public service measures, and oversees integrity affairs.

The Information Management Office handles the design of information systems and data management.

1. Maintain and manage irrigation and drainage facilities larger than minor turnout gates and drainage gates, including annual repairs, improvements, enforcement against violations, and flood emergency response.

2. Manage and regulate water diversion, conveyance, and distribution for systems larger than minor turnout gates and drainage gates.

3. Supervise and evaluate the work of water management teams.

4. Coordinate and resolve water-related disputes.

5. Implement water policies and manage canals.

6. Monitor and manage irrigation water quality.

7. Develop and execute irrigation plans.

8. Survey irrigation and drainage areas, including cadastral data.

9. Perform tasks assigned by the irrigation management organization.