Four emergency workers were attempting to reach people trapped by the flood waters near Pfaffenhofen in the region of Bavaria when their boat capsized.
Three of the crew managed to pull themselves to safety, while the fourth, a 42-year-old, was found dead in the water by other rescue workers at around 2:20 am (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," he said.
A rescue operation was underway to find another volunteer firefighter in Offingen, Bavaria.
The 22-year-old fell into the flood waters after his vessel capsized overnight, local police said.
Scholz is expected to visit the flood-affected regions area on Monday, with the German Weather Service (DWD) warning of more rain to come in the southern and eastern parts of Germany.
Heavy rains since Friday have led to flooding across the southern German states of Baden-Wuerttemberg and Bavaria, with thousands forced to evacuate.
In Bavaria alone, 3,000 inhabitants had to leave their homes as the flood waters rose, the regional interior ministry said.
Rail services between the cities of Stuttgart and Augsburg were also interrupted after a landslide caused a train to derail.
The front two carriages left the tracks near the city Schwaebisch Gmuend and slid into a car on a street next to the line, according to police. Neither the passengers nor the occupant of the car were injured.
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