The woman was found Monday evening in a creek near her house and police believe her death was probably due to the heavy rains.
Local news site Nordbayern.de reported that locals experienced flooded basements and overturned trees, and that several small fires had even been started by lightning.
One fire was sparked when lightning struck the roof of a single family house in Hirschau, with the damage estimated to cost some €50,000. Another building where fire wood was stored burned to the ground after lightning struck.
German weather service DWD predicted that Tuesday will see even more thunderstorms and hail for southern Germany, issuing high storm warnings for both Bavaria and Baden-Württemberg, mostly in the southeast regions.
DWD said that wind speeds in these areas could reach up to 80-100 kilometres per hour.
By Wednesday, the rest of the country will also be hit with rain, as the major western cities like Cologne are set to see storms, and the eastern capital of Berlin is also set to have a wet day.
Weather prediction for Wednesday: DWD.
Late May and early June saw some of the worst flooding in years in southern regions, with ferocious waters destroying villages, leaving 13 dead.