The article examines the problem of organizing state management of maritime and inland water transport, its system and structure, where the managerial and leadership role of the President of the Russian Federation in the system of management of the material subsector of maritime and inland water transport should be highlighted. The article explores the essence of federal agencies and services being under the jurisdiction of the Ministry, and notes the prospects for developing such management within the established organizational system and structure of state management of maritime and inland water transport.