The basic mission and responsibility of the Section is to ensure the execution of state administration and state professional supervision in matters concerning inland and maritime navigation, especially pursuant to Act no. 114/1995 Coll., On Inland Navigation, and pursuant to the changes and amendments to Act no. 455/1991 Coll., On Doing Business on the Basis of a Trades Licence (the Trades Licensing Act), as amended, and in matters concerning maritime navigation, especially pursuant to Act no. 61/2000 Coll., On Maritime Navigation.
The Section also has responsibilities related to conceptual and methodological contributions to the development of inland navigation; ensures the representation of the Czech Republic in international organisations, in as far as it falls within its powers; is the appellate body in administrative procedures; and processes background documents for the harmonisation of EU Law.
 
Ensures the execution of state administration and state professional supervision in maritime navigation and performs the role of the Maritime Authority.
 
Methodologically manages and assesses the work of the State Navigation Administration (Státní plavební správa) and the Czech Directorate of Waterways (Ředitelství vodních cest ČR).