Several people were still missing but police on Tuesday reported the rescue of a woman after she spent 52 hours in a tree she had climbed to escape the flood waters.
Police said they had located the 32-year-old in the forest near Neu-Ulm, Bavaria, with the help of a drone and a helicopter.
In the southeastern city of Passau, on the border with Austria, large parts of the centre were submerged by the rising waters.
The city, located at the confluence of the Danube and the Inn, declared a state of emergency as the rivers burst their banks.
The city had prepared for rising waters on the Danube since Friday, when the downpours that triggered the floods hit southern Germany, Passau mayor Juergen Dupper told journalists.
The coincidence of unexpectedly high water levels on the Inn as a result of rains on Monday was a situation the city "cannot stand", Dupper said.
"At the moment we can say there has been no human cost. That is very important news," Dupper added.
Elsewhere, in the southern region of Bavaria, police reported a woman had died after becoming trapped in her car in the floods.
Rescuers were unable to reach the 57-year-old after she told responders her car had slid off the road and was filling with water.
Her death brought the number to have died to at least five, with officials in Bavaria saying another six were missing.
Three people were found dead in their basements following the floods, while one rescuer was thrown overboard when his boat capsized and died.
Thousands of people in the regions of Bavaria and Baden-Wuerttemberg had to leave their homes as torrential rain from Friday sparked deadly flooding.
Rain continued to fall over the weekend into Monday, with districts across southern Bavaria declaring an emergency.
Some 60,000 rescuers were deployed to fight the flood and move people to safety.
Bavarian premier Markus Soeder said the regional government would make at least 100 million euros ($109 million) of support available to flood victims.
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