Thousands of people have been evacuated from their homes over the weekend in the southern regions of Bavaria and Baden-Wuerttemberg.
The situation continued to get worse overnight into Monday, with 800 people asked to leave their homes in the area of Ebenhausen-Werk, Bavaria, after a dam burst.
The district of Regensburg, which sits on the Danube, also joined a growing list to declare a state of emergency as the water rose.
Scholz was expected to visit the area of Reichertshofen, in Bavaria, close to where some of the worst flooding has been seen.
The chancellor will arrive in the flood zone around 11:00 am local time (0900 GMT) in the company of Interior Minister Nancy Faeser and Bavarian premier Markus Soeder.
On Sunday, a 42-year-old volunteer fireman was found dead after his vessel turned over during a flood rescue operation.
Another volunteer, 22, was still missing after his boat also overturned overnight into Sunday.
A search operation to find the missing rescue worker had to be stopped due to the exceptionally high waters and strong currents, local police said.
The search was set to resume Monday, if conditions improved.
The German Weather Service (DWD) lifted warnings of heavy rain and storms overnight into Monday in all the affected areas.
Some rain could however continue to fall in the areas of southern Germany already impacted.
The widespread flooding and continued rainfall had an impact on transport in the region with widespread train cancellations and delays.
Train lines leading from Munich to Stuttgart, Nuremberg and Wuerzburg were unusable as a result of the bad weather, rail operator Deutsche Bahn stated on its website.
A landslide near Schwaebisch Gmuend overnight into Sunday caused a high-speed train travelling between Stuttgart and Augsburg to derail, blocking the line. Nobody was hurt in the incident.
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