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The bureau has a director, a deputy director, and a chief for engineering, management, planning, and assets sections respectively, and a chief for secretarial, and accounting, personnel, and government ethic offices respectively as well.

The works section is responsible for surveying, designing, administration of works, and supervision of the construction.

The management section manages affairs of river surveying, drainage system, seawall management, and areas around rivers and seawalls. It also handles land acquisition for construction, prevention and crackdown measures of illegal cases.

The planning section conducts examinations of hydrology and fundamental information concerning planning, investigation, statistical analysis and management of information, and also the planning procedures for projects of river drainage and seawall renovation.

The assets section is responsible for supplies, control, delivery and management, and management of information and public lands.

The secretarial office manages documents, files, administration affairs, accounting, property management, research and evaluation, and other services that are not dealt with by all the other sections and offices. A secretary is appointed for the secretarial office.

The accounting office arranges annual auditing, accounting, and statistical affairs. The services that this office provides can be divided into three categories. The annual auditing services include approximation of total expenses, budgeting, supplemental appropriation, and budget allocation. The accounting services include accounting, accounting statement, budgets and expenditure handling, and annual accounting. The statistical services include running statistics of water-conservancy activities, and managing statistical data.

The personnel office handles personnel affairs.

The anti-corruption office is responsible for the anti-corruption cases.