No injuries were reported from the widespread storms, but more than 100 ambulances and rescue vehicles were dispatched across the country to respond to emergencies ranging from stranded motorists to house fires caused by lightning strikes.
In Braunschweig, Lower Saxony, water had to be pumped from numerous basements, with one tank leaking heating oil - causing a spillage of several hundred litres.
In the southwestern state of Baden-Württemberg, a stretch of the Rhine Valley railway line had to be temporarily closed after a train ran over a tree that had fallen onto the tracks.
In Saxony, traffic on the A72 motorway came to a standstill after the water level reached a height 30 centimetres.
Forecasters are predicting more storms for the weekend. On Friday night, heavy rain and thunderstorms are expected in the northeastern and southeastern parts of the country.
On Saturday, cloudy skies will give way to showers and thunderstorms across central and southern Germany over the course of the day, with the possibility of hail.
Temperatures will range from 20 degrees on the northern coastline to 28 degrees in eastern Brandenburg. Saturday night will bring possible thunderstorms, with temperatures between 13 and 17 degrees.
Sunday will start out partly cloudy and warm in eastern and southern Germany and more overcast in the west, where showers and thunderstorms will move in and travel eastward. Temperatures will remain on par with Saturday's highs and lows.
This year's weather conditions are being blamed for below-average crop yields in different regions in Germany. Wet conditions and heavy frost at the beginning of the year, followed by a dry spring with too little rain have dimmed the prospects for better crops, and the yields of wheat and barley are both down.
Meanwhile, some farmers in Germany aren't citing the weather, but four-legged pests for their crop losses. Field mice are getting the blame from Thuringia to Rhineland-Palatinate for crop damage. In Thuringia, farmers estimate that one-tenth of their yields will be lost because of the pesky rodents.
On some individual farms in Saxony-Anhalt, mice are being blamed for losses of up to 50 percent of the crops. In Bavaria, the mouse population has also grown, likely due to a milder winter.