The driver in Munster is believed to have died when his car came off a flooded road. It is thought he was swept away by the water.
A 76-year-old also died in his flooded cellar in Munster, North Rhine-Westphalia, overnight on Monday as flood water poured into cellars all over the region.
In subways and underpasses the water was over half a metre deep.
A woman suffered life-threatening injures in central Munster and had to be freed from her vehicle by emergency services after a falling tree struck her car.
In Greven, a town of 36,000 inhabitants, the town centre was closed to traffic after 60 litres of rain per metre squared fell within six hours, weather service DWD estimated.
Overwhelmed fire services registered more than 1,000 emergency calls from citizens, mostly due to flooded cellars. Eight hundred emergency workers worked through the night, with many places having to call in back up from unaffected areas.
Meanwhile, traffic chaos and long queues ensued after main roads including the A40 in Essen were flooded or closed due to fallen trees.
Parts of Baden-Württemberg and the industrial Ruhrgebiet were also affected by the storms, with cellars flooded. The DWD issued further weather warnings for Tuesday for central Germany.