Caught off guard by the outbreak of war, Ackermans & van Haaren lost several vessels in Poland: two dredgers sank in the port of Hel, and a hopper barge was lost in Gdynia. Société Générale de Dragage (SGD), the dredging division of CFE, faced similarly serious challenges. Both companies would subsequently combine their dredging activities to form Dredging International in 1974, laying the foundation for what would ultimately become DEME when it was established in 1991. During the conflict, the vessel Loire ran aground in Vlissingen, while other vessels were bombed by German aircraft as they attempted to flee to Dunkirk. Out of the sunken ships, Semois I, Samber I, and Schelde, only the latter was eventually salvaged.

The evacuation of the dredging fleet of Baggerwerken Decloedt, which was another company that would later form part of DEME, proved to be equally difficult given the challenging wartime conditions. On May 18, 1940, two convoys departed from Ostend and Zeebrugge. Only one vessel, Vlaanderen IX, reached Great Britain, where it was deployed as a firefighting ship during the war.

Other dredgers sought shelter in safe harbors in order to avoid attacks by German Stukas, which in turn were targeted by British Spitfires. Archival footage shows how the cutter suction dredger L’Yproise lay between a small bucket dredger and the hopper dredgers Vlaanderen IV and Vlaanderen V. During the retreat ahead of the German invasion, Vlaanderen IV was heavily damaged in May 1940. Laden with refugees, the vessel ran aground on the beach of Calais.