Two children aged one and 10 years are missing after a rescue boat they were in capsized in River Tana, in Idsowe village.
The children were among five others who had been rescued from the marooned Galili village on Friday, having spent a night on roof tops.
County Red Cross Coordinator Jerrald Bombe told the Nation that the team had just rescued the five and were headed to safety when the water currents overpowered the boat overturning it.
"They were headed to safety but the water became very rough as it moved fast. With the boat moving in the opposite direction, it overturned due to strong currents,” he said.
The team immediately managed to rescue two to safety as three went missing in the water.
A team of Red Cross expert divers were later deployed to help with the search in the crocodile-infested river.
After hours of searching, one child was found unconscious late in the night trapped by reeds in the river.
The team immediately rescued him and took him to Garsen Hospital where he is said to be in stable condition.
On Saturday morning, Mr Bombe there was hope of finding one of the missing children alive as the girls who was rescued and resuscitated told the team that her sister managed to get to a tree along the river bank.
The boat that is said to have been hired by a local politician to support the rescue mission was pulled out of the water for repairs.