The 61-year-old man was working on an electrical appliance while water was being pumped out of his cellar. His death is the third flood-related fatality in the eastern German state. His traumatized wife was taken to the hospital.
The authorities brought 150 people to safety in Stendal, Saxony-Anhalt overnight after a breached dyke near Fischbeck allowed the floodwaters to gush towards their homes. "Despite several attempts to save the place, it just wasn't possible," said an emergency services spokeswoman.
In Schleswig-Holstein in the north, fears focused on the town of Lauenburg, 40 kilometres (25 miles) southeast of Hamburg, where the Elbe River was expected to peak on Wednesday.
The river had already risen more than double the normal. The old quarter of the town had its power cut and some 400 people had to seek higher ground. Some streets were already submerged in 30 centimetres of water, according to local official.
Chancellor Angela Merkel was expected to survey the situation in Lauenburg and in nearby Hitzacker later in the day.
Downriver the Elbe stabilised as towns and cities remained in a state of alert, particularly in Magdeburg, the capital of Saxony-Anhalt, where more than 20,000 have had to seek emergency shelter.
Rail traffic between Berlin and cities in the west has been redirected due to submerged tracks and the closure of a bridge in Saxony-Anhalt in the centre of the country, leading to delays of up to two hours on some routes.
The authorities have yet to publish an official figure on the cost of the deluge but a private ratings agency said the figure could surpass €12 billion ($16 billion) in Germany alone.
The German Agricultural Association said sodden fields, destroyed crops and damaged equipment brought losses of €405 million, according to a preliminary estimate published Tuesday. Around 305,000 hectares (750,000 acres) of fertile farmland were submerged as the floodwaters worked their way north, with Saxony-Anhalt in the centre of the country seeing about one-third of the total damage.
Officials in Bavaria, which experienced the worst of the flooding last week, said the brown waters had wiped out around 60 percent of the vegetable harvest.