Several streets around Hamburg’s fish market were left under water in the early hours of Sunday, as the waters of the river Elbe surged to close to three metres over their usual high-water mark.
Cars were damaged, while rescue teams used the opportunity to go on exercise in the low-lying district.
Storm Nadia swept in from Scandinavia on Saturday evening, bringing with it hurricane-force winds.
At Kiel lighthouse a blast of 122 km/h was recorded. Fierce winds were felt all the way down to Berlin and Saxony in the east of the country.
Bild newspaper reported a fatality in Brandenburg, where a man was struck by a billboard that had been ripped up by the wind.
And Hamburg fire services were in constant operation, tackling over 300 call outs over the course of the night.
As water levels surged, a ship got caught under an autobahn bridge in the harbour, leading to a rescue operation in which two crew members were taken from the boat.
Separately, a cargo ship was left flailing against the strong wind and waves around 16 nautical miles off the North Sea coast from Cuxhaven.
After the engine proved incapable of withstanding the storm, tug boats were sent out and after six hours, the ship was finally brought under control.
“If we had not intervened, the ship would have become a risk to the coast,” a coast guard spokesperson said.
There were also massive disruptions to rail traffic in northern Germany due to the storm damage.
Early on Saturday evening, Deutsche Bahn suspended long-distance trains in Hamburg, Schleswig-Holstein, Lower Saxony, Mecklenburg-Western Pomerania and Bremen.
Deutsche Bahn said a resumption of normal service was dependent on when the wind died back down.
The timeline for when the trains would run again as planned depended on the further course of the storm, a spokesperson for the railway said.
According to the Federal Maritime Agency, the North and Baltic Sea coasts could see more flooding during the day on Sunday. Dangerous tidal surges could also affect the Weser and Elbe river close to their mouths.