Three children are missing after they were swept away by water in river Mwache in Kinango subcounty, Kwale.
Two others were rescued.
The five had gone swimming in the swollen river. The children are aged between 12 and 14 years.
Chief Benson Kalimbo confirmed the incident.
"I have just received news from my assistant that some children have been swept away by water," he said.
Residents are helping look for the missing children.
Residents said the children were warned to get out of the water when the rain started but they went back and the current overpowered them.
In the past three days the county has experienced heavy downpours.
Kalimbo cautioned residents against trying to cross flooded rivers.
He urged parents to monitor their children and keep them away from water paths.
The flooded river Mwache has also interfered with transportation along the Mazeras-Gandini-Kinango road.
Kalimbo advised residents living in low-lying areas prone to floods to monitor rising water levels and evacuate to higher grounds.
In 2017, more than five people perished in various parts of the region after they were swept away by raging floods, three children were among the dead.
More than 1,500 families were also left without homes after their houses were submerged after dams and rivers burst their banks.
In 2019 several houses, farms and livestock were swept away by floods in Vanga and Mwangwei villages.
