In the early hours of 14 January 1993, it capsized and sank in 27 metres (88 feet) of water off Cape Arcona off the coast of Rügen in the Baltic Sea while sailing towards Ystad with 64 passengers and crew.

The sinking of Jan Heweliusz is the deadliest peacetime maritime disaster involving a Polish ship.

Prior to its sinking, Jan Heweliusz had been involved in 28 incidents, including collisions with fishing boats, listing, engine failure and the aforementioned fire in 1986.

It had ballast problems and had also damaged its hull in Ystad during docking, but this was not reported to the port authorities and only makeshift repairs were made.

In 2005, the European Court of Human Rights in Strasburg ruled that the official investigation of the sinking was not impartial and granted €4,600 in damages each to eleven relatives of the victims.