[1] Sloten originated in the thirteenth century as a settlement at a stins of the Van Harinxma thoe Slooten family.

During the siege of Sloten in 1523, where Frisian and Gelderland troops were stationed, the Hollandic nobleman Jan II van Wassenaer was fatally wounded.

Sloten is located on the once important waterway from Sneek to the former Zuiderzee, overseeing access to the Hanseatic cities on the IJssel.

The country road ran via Doniawerstal over the gaasts (sand ridges) via Sloten, where the waterway could be bridged, to Gaasterland and on to Stavoren, which in the Late Middle Ages had been a large and important trading town.

At the end of World War II, the Germans blew up the bridge over the Ee to slow down the progress of Canadian troops.

In the 1970s, a marina was built on the south side of the city where a number of water sports companies are located.