In Burundi, entire villages in the west of the city of Bujumbura have been inundated by water, after days of torrential rains caused water bodies to burst their banks.
The floods have caused dispalcement, with families abandoning their homes to look for dry ground.
River Rusizi, which runs along Burundi's border with the Democratic Republic of Congo was the first to overflow, before Lake Tanganyika's already rising waters spilled over.
"All the children's notebooks were flooded. The clothes and other materials. We didn't save anything," said Francoise Habonimana as she washed the few clothes she was able to salvage with her daughter.
The most affected areas are the poor, low-lying neighborhoods of Bujumbura where proper drainage systems are virtually non-existent.
Experts say entire villages need to be moved for the area's destroyed eco-system to be rehabilitated.
"We must relocate this population because there is no solution", said Bernard Sindayihebura, a geographer and university professor.
"There are zones where construction must be prohibited to avoid these enormous economic losses," he added.
Floods are a recurrent problem in the east African country. Burundi's topography and the absence of proper road and drainage infrastructure means Bujumbura's residents have to flee their homes almost every rainy season.
Unusually heavy rains have also caused flooding in Somalia, Kenya and Uganda.