The body of the 43-year-old, whom rescuers had been looking for since Sunday, was found in a basement in the Bavarian town of Schrobenhausen, police told German news agency dpa.
A firefighter was found dead in nearby Pfaffenhofen on Sunday after an inflatable boat he and colleagues were using capsized.
Persistent heavy rain led to widespread flooding in the southern states of Bavaria and Baden-Wuerttemberg over the weekend.
The floods caused extensive transport disruption, with long-distance rail routes to Munich from the north and west out of action on Monday.
Scholz visited Reichertshofen, north of Munich, inspecting a sandbagged river bank and meeting regional officials including Markus Soder, Bavaria's governor.
Soder said the situation "remains critical and tense", with water receding in some places but new flooding and evacuations elsewhere.
He noted that water levels are expected to rise in the city of Regensburg and further down the Danube.
Scholz said "this is not just one event like there have been for centuries", and added that a succession of floods in recent times shows "we cannot neglect the task of halting man-made climate change".
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