The 42-year-old died after his rescue ship capsized near Pfaffenhofen in the region of Bavaria.
Four emergency workers were attempting to reach people trapped by the flood waters, when their boat turned over.
Three of the crew managed to pull themselves to safety, while the fourth was found dead in the water by other rescue workers at around 2:20 am local time (0020 GMT).
"I am saddened by the death of a firefighter in Pfaffenhofen. My thoughts are with his family and colleagues," Chancellor Olaf Scholz said on X.
"We owe thanks and respect to the rescue workers and helpers who are fighting the consequences of the floods in many places," Scholz said.
Heavy rains from Friday onwards have led to flooding across the southern German states of Baden-Wuerttemberg and Bavaria.
German rail operator Deutsche Bahn said on Sunday the rail link between the cities of Stuttgart and Augsburg was closed as a result of the severe weather.
Two carriages of a high-speed train travelling on the line came off the rails after a landslide, according to local media reports.
None of the passengers on board were injured in the incident late on Saturday, close to Schwaebisch Gmuend.
Several districts in Bavaria have declared emergencies as a result of the high waters.
The German Weather Service (DWD) warned of more heavy rain to come in southern Germany on Sunday.
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