During the Second World War, in the period between 1942 and 1944, the Jan Nieveen was used to smuggle hundreds of Jews from the western part of the country to Fryslân, from Amsterdam across the IJsselmeer to Lemmer. Among them were many of the 210 so-called 'crèche children' from Amsterdam. They sometimes had to hide underneath the benches and behind the luggage. Or they had to be dressed up sometimes, when things got dangerous. Skipper Haije Bouwman knew about them, but pretended not to notice.  

From Lemmer, one route went to Sneek and one to Leeuwarden. In Sneek, the Baptist vicar, his wife and the curate received the children and arranged shelter for them with the help of the Baptist communities of Sneek and Leeuwarden. The children were lodged with families across Friesland, where they stayed until the end of the war.  

In addition to the transport of 'smuggled children' to Friesland, the Frisian shipping industry also played a major part during the Hunger Winter of 1944-1945. Driven by hunger, many young evacuees from the western part of the Netherlands made the crossing of the IJsselmeer, to be received in Friesland. Vice versa, food was also sent by the resistance to the starved west, such as for example thousand cheeses which the occupiers had earmarked for Germany but were stolen by the resistance.  

By the end of the war, many German soldiers used the ships between Friesland and Amsterdam to escape the advancing Canadians. 

Ships were sometimes also used for acts of sabotage, such as for example at Kingmatille, where a barge was sunk by the resistance to block the waterway between Leeuwarden and Harlingen.  

Frisian ships played an important part in Burgum when seven of them had to form an emergency bridge to replace the destroyed bridge at the Burgumerdaam. 

The Frisian Maritime Museum is a museum about the history of the Maritime industry in Friesland, the ice sports, and the history of the city of Sneek. During the war, the building at the Kleinzand was inhabited by the Lever family. Father Hendrik Jacob, mother Berendiena, sons Jan and Henk and daughter Meta were all active members of the resistance. They distributed illegal papers and helped Jewish compatriots find a place where they could go in hiding. This proved fatal for the male family members. Father Hendrik died in Dachau, son Jan was killed in a gunfight in Eenum (Groningen), and Henk's life was ended by a firing squad in Kamp Vught.