Near the end of the war, as the German army was retreating on all fronts, Nazi Germany began to evacuate the camps near the eastern front and march the inmates westwards. Not yielding despite the visible defeat, the Nazis were determined to prevent the survivors from falling into the Allied hands. During these "death marches" prisoners were forced to march long distances in bitter cold, with little or no food, water or rest. Those who were unable to continue were shot along the way. Liberation was close, yet for the victims this was the beginning of a new phase of terrible suffering. Many lost their lives in these last months and days of the war.

In the end of January 1945 the evacuation of nearly 50,000 prisoners of the Stuthoof camp system began. About 5,000 inmates from the sub-camps were marched to the Baltic Sea coast, where they were forced into the water and machine-gunned. Others were marched to eastern Germany, where they were cut off by advancing Soviet forces and forced back to Stutthof. Thousands died on the way. In late April 1945, the remaining prisoners were evacuated to Germany by sea. It is estimated that over one half of the prisoners died during the evacuations.