Some five thousand people in Niger lost their homes and crops after the River Niger burst its banks at the weekend.
The West African country is already suffering from severe food shortages caused by recent drought.
Another 20,000 people are at risk of displacement in the event of further heavy rains, UN officials have warned.
Heavy rainfall has also caused flooding across other parts of West and Central Africa and threatens to worsen the food crisis in the region, the UN said.
Millions of people are without food in the region after droughts over the last year depleted stocks, the UN World Food Programme warned.
"Rain in the Sahel is much welcome but it needs to be properly distributed over time and over space which is the major issue now," the WFP's Naouar Labidi told Reuters news agency.
The BBC's Idy Baraou in Niger's capital, Niamey, says many more houses in and around the city are in danger of collapsing and residents fear that more heavy rain is still to come.
The UN said that 30,000 animals had died in the flooding and carcasses could be seen floating near water points, spreading further fears of outbreaks of waterborne diseases.
Meanwhile, on Monday the authorities in Ghana issued a flood warning for three northern regions because of rising water levels at two dams in neighbouring Burkina Faso.
According to the UN's Irin news agency, 40 people have already died in flooding in Ghana in June and July.
In Burkina Faso, the agency reported that 14 people had died last month in floods and many people were sleeping in schools and other public buildings.
Northern Chad in the Sahara desert has recently recorded the heaviest rain in 50 years and hail stones the size of eggs destroyed crops in central Guinea in July, Irin said.
The International Federation of the Red Cross says it is providing aid to flood victims in the Central African Republic and in Ivory Coast, where there have been mudslides.
On Monday, at least 13 people died - most of them children - in the Sierra Leonean capital, Freetown, when a building collapsed during a mudslide, following torrential rain.