The man was in a rubber dinghy with three other rescuers in the town of Pfaffenhofen in Bavaria late Saturday when the vessel capsized.
His body was found early on Sunday, according to a spokesman for the Pfaffenhofen district office.
The three other firefighters were rescued. They had been on their way to rescue a family in the severely flooded area. There were no details on what happened to the family.
Fire brigades and other emergency helpers have been working constantly since the heavy rains, which have not stopped since Friday.
Germany's army has stepped in to help as rivers in the region have swelled. Many hundreds of people have been evacuated as well as a prison in Memmingen to the west of Munich, with 100 prisoners taken in by institutions nearby.
More than 100 people were reportedly rescued on Saturday with more storms forecast for the area. (AP PHOTO)
Some regions in southern Germany have recorded more rain within 24 hours than normally falls over a whole month, the German Meteorological Service (DWD) reported.
Kisslegg in the south-western state of Baden-Wurttemberg recorded 130mm on Friday alone, the DWD reported. The region normally reports 118mm per month at this time of year.
In Bad Worishofen in the neighbouring state of Bavaria, 129mm fell within 24 hours, by comparison with a monthly average of 101mm.
The Swabian Alps south of Stuttgart, as well as the region around Augsburg, Nuremberg, Bamberg and Regensburg were reported to be at particular risk from thunderstorms on Sunday.
Two dams on the Paar River, a tributary of the Danube, had been breached in the region, leading to the closing of nearby stretches motorway.
German Chancellor Olaf Scholz on Sunday expressed his thanks to the emergency services.
"The death of a firefighter in Pfaffenhofen has shocked me," he posted on the X messaging service, adding that his thoughts were with the firefighter's relatives and colleagues.
Scholz was to visit the region on Monday.
Bavarian Premier Markus Soder said some 40,000 emergency services staff had been deployed across the state, Germany's largest by area.
"The most important thing is to arrange their relief over the hours ahead," Soder told journalists in Reichertshofen in Upper Bavaria, which lies just to the north of Pfaffenhofen. He expressed concerns for the safety of rescue workers who had been working for too long without a break.
A fire services spokesman said the flooding in the region was unpredictable and was the most extreme seen to date. Some 4600 rescue workers had been deployed in the immediate region, he said.
Soder appealed to residents to pay attention to alerts issued via their mobile phones.
"If you hear the alert on your phone with the call to evacuate, don't pack your suitcases to take all kinds of things with you, but just go straight out," he said.
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