The Danube Hydrographical Service was established in 1935 within the structure of the Ministry for Railways, with headquarters in the city of Lom and the mandate to maintain the navigational waterway, create maps of the Danube River, and conduct hydrometeorological surveys in the Bulgarian section of the river. The year after the ratification of the "Convention for the sailing regime on the Danube river" in Belgrade in 1948, the "Danube Hydrographical Service" passed over to the Ministry of Defense - Danube Fleet - Ruse. In the year 1953, the service was reinstated as a part of the Ministry of Transport, information technology and communications, and the Navigational Waterway Office in Ruse was established with a task to maintain the navigational waterway in the Bulgarian section of the Danube river. Its activity at that time did not include the development of hydrographical and hydrological studies of the river regime. In 1955 the Navigational Waterway Office passed over to the Bulgarian River Fleet. On April 1, 1956, the Council of Ministers adopted a decree, by the force of which the Navigational Waterway Office was restructured into the "Administration for the Maintenance of the Navigational waterway and Exploration of the Danube River" with headquarters in the city of Ruse within the Ministry of Transport, information technology and communications.
In December 2, 1999, by force of decree No 212 of the Council of Ministers, the Administration was transformed into the Executive Agency for Exploration and Maintenance of the Danube River.