The German Weather Service declared on Saturday morning that its extreme weather warning was over, as the storm moved on towards Russia.
But in its path it left serious disruption and at least two fatalities.
In Hamburg, where lower-lying parts of the city are regularly flooded during storms, authorities measured the highest water level in close to a decade.
At the water gauge in St Pauli the tide rose to 3.75 metres above the average high tide mark on Saturday morning.
The famed Speicherstadt district of Hamburg was flooded and two men who had been trapped there had to be rescued and taken to hospital.
The strongest blast of wind measured during the storm was a 143 km/h gust in the coastal town of Büsum on the North Sea.
Police confirmed victims of the storm in North Rhine-Westphalia and Lower Saxony.
In Lower Saxony, a man fell from the roof of a barn during the storm and died. The 68-year-old was trying to repair the damaged roof on Saturday night, police said. But he broke through the roof and fell around ten meters.
In North Rhine-Westphalia, a motorist died on Friday evening near Altenbergewhen when he crashed his car into a tree that had fallen across the road. The 56-year-old died at the scene of the accident.
In Bremen, a 55-meter crane collapsed onto an office building that was under construction. “It looks devastating,” a fire department spokesman said.
A truck that was passing by was also hit by the crane but the driver escaped uninjured.
Rail traffic in northern Germany and northern parts of North Rhine-Westphalia was still severely restricted on Saturday morning, according to Deutsche Bahn.
Long distance rail in most of the north of the country was still on hold on Saturday morning.