Hamburg's famous fish market was flooded as water levels in the Elbe river that flows into the North Sea rose by 5.2 meters (17 ft) above normal levels, Reuters reported.
The German weather service had warned of hurricane-force wind in the north that could reach speeds of almost 100 kilometers (60 miles) per hour.
Firefighters in Hamburg responded to 450 emergency calls in the night between Saturday and Sunday.
Fallen trees that had blocked railways and roads were cleared and two men were rescued after a barge got stuck under a bridge in the northern city, emergency services said in a statement.
German public broadcaster NDR said several communities near the city of Wismar east of Hamburg experienced power outages.