“The situation has got dramatically worse in the last few hours. The whole centre of town has been flooded by the [river] Altbach,” Walter Czech, mayor of Triftern bei Pfarrkirchen in the Rottal district, told DPA.
Neighbouring Anzenkirchen was also badly affected by floods.
Triftern, a town of just over 5,000 people 35km south-west of Passau on the Austrian border, was not the only place to be struck by severe flooding.
Leipzig, Saxony's largest city, has also seen high waters block the entrance to the emergency room at the Elisabeth Hospital.
Train traffic between Saxon capital Dresden and the Czech Republic was briefly halted after a mudslide.
And firefighters in Bremen and Hanover were kept busy pumping out flooded cellars overnight as heavy rain swept into low-lying parts of the cities – including the Bremen fire service's own underground gym.
The German Weather Service (DWD) currently has serious weather and storm warnings in place across eastern Bavaria and in a swathe running from the northeast coast, over Hannover and all the way into North Rhine-Westphalia and Hesse.
Large parts of Saxony and Thuringia are also covered by the alerts.
Schoolkids can't get home
In Bavarian town of Triftern, around 250 schoolchildren cut off from their homes by the water face a night sleeping in the gym.
“Luckily the school building is on a hill,” mayor Czech said.
So far no-one has been hurt in Triftern, he went on, and emergency responders including firefighters and river rescue were on the scene.
A second group of 20 children were stranded on an island during a school boat trip, with one girl being treated for shock and another for hypothermia.
“Everyone who's available”, including firefighters and volunteer aid workers, has been sent to the flood area, police said.
Two helicopters are also being sent to rescue people who have been marooned in their houses in the Triftern area.
Eyewitnesses told broadcaster Bayerische Rundfunk that bridges and roads had been completely swamped and rivers had broken their banks.
In Passau river gauges stood at high levels on Wednesday afternoon, with the Danube exceeding its first warning level and the Inn just 40 centimetres below its own.
Some streets had to be closed in the city on the Bavarian-Austrian border for fear of flooding.
Baden-Württemberg picks up pieces
News of the flooding in Bavaria comes just as neighbouring Baden-Württemberg is getting to grips with the damage caused by heavy rain and storms on Sunday evening.
In Braunsbach divers were searching underwater for the bodies of people who might have been trapped in their cars by sudden violent floods.
State minister-president Winfried Kretschmann is also expected in the town today to inspect the damage.
Four people have been reported dead in floods since Monday.
Other parts of Germany, including North Rhine-Westphalia and Thuringia, also suffered flooding on Monday and Tuesday.