After days of continuous rain, rivers have overflowed their banks in many areas of Baden-Württemberg and Bavaria, resulting in thousands of people having to leave their homes.

Chancellor Olaf Scholz and Interior Minister Nancy Faeser (both SPD) were set to visit flooded areas on Monday. 

The situation was particularly critical on Monday morning in the two districts of Rems-Murr and Ostalb in Baden-Württemberg. Due to rising water levels, residential areas were evacuated in Abtsgmünd (Ostalbkreis). Residents were accommodated in emergency shelters and schools were closed.

Danube water dangerously high 

In Bavaria, authorities are still far from giving the all-clear. Although the floods are slowly receding in many places on the tributaries of the Danube, continuous rain is increasingly affecting the Danube itself.

The city of Regensburg declared a state of emergency on Monday as the water level of the Danube exceeded the highest reporting level of four, according to the Bavarian Flood Information Service (HND).

The water levels at the Eiserne Brücke measuring point reached 5.80 meters in the early morning hours. Last Tuesday the average levels hovered around 2.70 meters. According to experts, during the last major flood on June 4th, 2013, water levels reached 6.82 meters.

The river is expected to reach the highest reporting level in Passau on Monday evening. 

Several districts and cities in Bavaria declared a state of emergency at the weekend.

Many schools and day care centres are closed across the region on Monday, while emergency care is being set up for some younger school children.

READ ALSO: Forecasters warn of further heavy rain in flooded southern Germany

Search continues for two people

Emergency services are searching for two people.

A 22-year-old is missing after being out in the Günzburg district, Swabia, on a DLRG water rescue boat in the early hours of Sunday. The boat, which was manned by five emergency service volunteers, capsized at around 2.50 am due to strong currents. Four of the five on the boat were able to save themselves, but the search is continuing for the fifth helper.

A woman has also been missing since Sunday in Schrobenhausen in Upper Bavaria. Rescue workers suspect she was in a flooded cellar. Due to the dangerous situation, helpers were unable to search for her until Sunday evening. A police spokesman was unable to say on Monday whether she had been found.

It comes after one person was confirmed to have died. The 42-year-old firefighter died after a rescue boat 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.

Rail traffic in the south severely affected

Due to storm damage, rail travel in the south of Germany is severely affected on Monday.

Deutsche Bahn advised against anyone travelling to affected flood areas and recommended postponing all non-essential travel.

Long-distance train services cannot currently reach Munich from the north and west. Local transport in Bavaria is also severely affected.

READ ALSO: The trains cancelled in Germany due to severe flooding 

Forecasters say further thunderstorms are possible with lots of rain

The German Weather Service (DWD) lifted all severe weather warnings for extreme thunderstorms with heavy rain for Germany early on Monday.

However, there are still areas expected to see showery rain with the potential for heavy rain and moderate storms, especially in southern Germany. From midday onwards, areas south of the Danube and the Bavarian Forest will be particularly affected, and severe weather is also possible.

By the evening, storms could gradually spread southwards, as far as the Upper Rhine and the northern Alpine foothills.