One of the victims died after a house collapsed under heavy rains in the coastal city of Mombasa, police said, while the second was swept away by floods in Meru County in central Kenya. Emergency workers were searching for a third person believed to have drowned in Isiolo, in the country's north.
Kenya’s Meteorological Department had earlier warned of above average rainfall until Monday.
"Flood waters may appear in places where it has not rained heavily especially downstream. Residents are advised to avoid driving through, or walking in moving water or open fields and not to shelter under trees and near grilled windows when raining to minimize exposure to lightning strikes," read the alert.
In Mombasa, heavy rains caused flash floods, which swept away homes and businesses. Videos showed cars submerged in flooded roads, while in the northeast, a major road linking Wajir and Mandera counties was completely cut off leaving motorists stranded.
Dramatic footage also emerged Thursday of a wildlife conservancy chopper crew rescuing eight people who were in a truck that was being swept away by raging floodwaters in Samburu county.
Heavy rains were also reported in the neighboring countries of Tanzania and Somalia, where the International Federation of Red Cross and Red Crescent Societies said "several homes have been inundated and bridges damaged."