Meteorologists expect more heavy rain to hit South Sudan and other east African countries.
More than 600,000 people have been forced to leave their homes in South Sudan, IRC says.
On Wednesday, South Sudan’s President Salva Kiir declared a state of emergency.
Humanitarian agencies say things are particularly bad in Pibor, in the east of the country.
“The situation is extreme. The town is now submerged in water completely,” Médecins Sans Frontières’ emergency coordinator in South Sudan, Edi Ferdinand Atte, told BBC Focus on Africa.
The deputy head of the UN’s humanitarian coordination office in South Sudan, Andrea Noyes, said that aid workers are wading through the waters to help flood victims.
“We are having to move around in water up to our knees or up to our thighs to reach people in need,” she said.
Meteorologists expect more heavy rain to hit Somalia on Saturday exacerbating the problems caused by flooding in the country.
It has already been called the worst flooding in a lifetime by Action Against Hunger regional director Hajir Maalim.