In Allgäu in Bavaria, the fire brigade were mobilised several times because of fallen trees and swamped cellars, according to Bavarian radio station BR24, although the situation eased quickly.
And in Baden-Württemberg, there was flooding at the main station in Stuttgart because the water couldn’t drain quickly enough while some streets in Heilbronn were flooded.
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However, according to a report by southwest German broadcaster SWR, there was no major damage.
In the west of the country, the fire brigade reported a quiet night in the flood areas in Rhineland-Palatinate and North Rhine Westphalia.
The situation remains tense, however, with local thunderstorms forecast in some parts of Germany from midday on Sunday — most likely south of the Danube.
Further heavy rain and hail were also possible again, according to the German Weather Service (DWD), which publishes storm warnings.
The latest storms came just days after parts of the country were hit by devastating floods after torrential rains that ravaged entire villages and left 180 people dead, hundreds injured and with many still missing.
The flooding also caused damage in Belgium, where 37 people died, Luxembourg, the Netherlands and Switzerland.