The police in the southern German state said on Monday that rescue services received hundreds of calls to deal with flooded cellars and roads.
There were no initial reports of injuries but damage could be substantial after the storm brought strong winds and heavy precipitation.
A bolt of lightning struck a high-tension wire near Jandelsbrunn in Freyung-Grafenau county cutting power to an unknown number of households.
In Lower Bavaria there were 130 rescue calls within three hours. The city of Passau was particularly hard hit, as felled trees, flooding and small landslides blocked road and rail traffic.
The railway in Swabia between Günzburg and Ichenhausen was closed for more than three hours after the tracks were completely flooded by heavy rain. The authorities received 300 emergency calls in just two hours in the region.
The weather also swept over Nuremberg, but fortunately no one was hurt after a tree fell on top of a car.