Emergency workers in Mozambique have begun an operation to rescue thousands of people trapped on islands in the Zambezi river by rising flood waters.
Crops have been destroyed and villagers living on higher ground are building temporary shelters for people whose homes have been washed away.
Meteorologists have predicted no let-up, with more storms forecast for Mozambique, Zambia, Zimbabwe, Malawi.
Aid agencies are warning of food shortages and waterborne diseases.
The number of people affected by the floods is unclear but an estimated 50,000 people have been evacuated so far in Mozambique.
The World Food Programme (WFP) says it is still feeding 250,000 people there who lost their crops in last year's floods.
Most of those are affected again, and the WFP expects the numbers to rise even further.
From its head waters high in Zambia and Zimbabwe to the river mouth on Mozambique's Indian Ocean, the Zambezi river valley is a sodden mess.
In Mozambique, a few major towns like the provincial capital of Tete are under water but it is the tens of thousands of villagers in small, isolated settlements who are suffering the most.
Six people are known to have died - four drowned and two were killed by crocodiles.
The BBC's Peter Greste, who is in Caia where the main relief effort is being co-ordinated, flew over the area and described the roofs of countless huts dotting the water like lilies.
He said people displaced by the heaviest rains in a decade were wading through what used to be roads.
Working with soldiers and international relief agencies, Mozambique's National Institute of Disaster Management is using boats and helicopters to move those affected to temporary accommodation centres.
It is not clear when the situation will begin to improve; the rains are still falling in the catchment area and the water will take time to flow down.
Thousands of people in the region have been displaced
The wet season is also in its early days but the Zambezi is rapidly approaching the 7.6m (25ft) level that it reached during disastrous floods in 2000, when half a million people fled their homes.
In Zambia, the government has appealed for $13m (£6.6m) in foreign aid to help deal with the effects of flooding, which officials say has displaced thousands of people and caused extensive damage to infrastructure.
In low-lying areas of Zimbabwe, flooding has destroyed homes, livestock and infrastructure, aid agencies report.
Heavy floods have also destroyed homes and crops, displacing thousands of people in southern and central Malawi.
The Malawian government is warning people to relocate from flood-prone areas, but many have been reluctant to leave their farms.
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