Southern Bavaria around Munich was particularly hard hit, with police and fire fighters being called out more than 170 times to deal with flooded cellars and garages. Nobody was injured, despite the chaos.
Water washed away roads and sidewalks throughout the region, sending local officials scrambling to respond.
“The storm is the worst in recent years,” said Friedhelm Liwack, from Auetal, in Lower Saxony.
By Thursday afternoon, the situation had calmed, though there was a considerable mess to clean up.
At one Munich shopping centre, water was one metre deep in places. Twenty shops remained closed. Authorities pumped water from a city centre hotel and the city museum. The chaos caused traffic jams on water-filled roads.
The storm started about 5 am with thunder and lightning. At times, 52 litres of rain fell per square metre each hour, according to the German Weather Service (DWD).
The DWD predicted that the worst of the storms was over, though it predicted cool and soggy weather throughout Germany for the rest of the week. Thunderstorms are expected to break out from time to time.