The Autonomous Port of Paris is a public institution under the responsibility of the Ministry for Ecology, Energy, Sustainable Development and the Sea.

It is managed by a 3-member management committee headed by Hervé Martel, its Managing Director. This committee defines and applies corporate policy to promote goods and passenger transport on the waterways and reduce road traffic pressure in Ile-de-France, and organises and supervises the work of the various Departments and Agencies.

 
The Autonomous Port of Paris is organised geographically into 5 Port Agencies. These agencies provide a strong local presence and oversee the development of the 70 public ports in Ile de France, as well as offering support for private ports through close contacts with local authorities and businesses.
Functional Departments handle strategic development and general administration, in liaison with the Port Agencies.
Each of these Departments is coordinated by a member of the general management.