A 72-year-old woman drowned overnight after her husband lost control of their vehicle, Fabrice Pierart, a local firefighter, said.
A second victim, who was on his way home, was found just yards away, Lt Pierart added.
The mayor of Beaumont, Charles Dupuis, said: "This is a catastrophe for our region." Other offocials described the flooding as the worst in 50 years.
Belgium's national weather service said that in two days the country absorbed as much rainfall as it normally gets in a month.
Rivers and creeks overflowed in western and central area, causing building basements and streets to flood in scores of towns and cities. Rail traffic was seriously interrupted yesterday.
Local authorities called in the army and civil protection teams to reinforce the firefighters who had been working overnight.
The situation appeared particularly serious in the Brabant region, just outside Brussels.
However, prime minister Yves Leterme said there was no need to declare a national emergency, but added that his government was monitoring the situation closely.