The district of Steinfurt in North Rhine-Westphalia called a state of emergency on Friday morning due to the violent weather.
A rainfall reservoir threatened to burst its banks and flood an industrial area in Rheine, forcing emergency workers to bolster it with sandbags.
And a tornado touched down in Bad Salzuflen causing considerable damage. The twister ripped off the roofs of two houses and uprooted trees with metre-thick trunks.
The city of Osnabrück called a state of emergency around 4 am after the Hase River rose 2.4 metres higher than normal due to torrential rains. The A30 motorway between Sutthausen and the junction towards Hannover was closed early on Friday.
The storm front halted rail traffic between Münster and Osnabrück. Deutsche Bahn warned of delays in the region.
The heavy rain also caused problems in parts of southwestern Germany, flooding cellars and streets.
Up to 60 litres of rain per square metre fell in Heidelberg in just one hour, forcing street closures in parts of the Rhine-Neckar region. Manhole covers were dislodged by the immense water pressure. Several trees were toppled and rescue services received around 300 calls asking for help.
A youth group camping in the Morretal region near Buchen was caught in a flash flood and their camp had to be evacuated. The 40 children and their counsellors found refuge with the Bundeswehr in Walldürn.
There were also temporary power blackouts in several parts of the state of Baden-Württemberg due to falling trees and flooding.