At least two people died after they were swept away by floodwaters in Illaut, Samburu North, on Tuesday evening.
Daniel Lesaigor, Samburu County's Special Programmes Chief Officer, said the bodies of the six-year-old and 30-year-old were found.
"[The two separate incidents] resulted from Monday's heavy downpour. The village was swept by flash floods. The rest of the people are safe," Mr Lesaigor told the Nation.
Disaster management teams rescued tens of people who had been marooned by the raging waters.
Mr Lesaigor said hundreds of families in the north were left homeless.
"Their houses (manyattas) were destroyed completely," he said.
Heavy rains have caused flash floods and left a trail of destruction in many parts of Samburu.
Mr Lesaigor said more than 250 goats, five herds of cattle and an unknown number of camels were also swept away.
Elsewhere, Samburu Lodge hotels were marooned by floodwaters after River Ewaso Nyiro broke its banks following the heavy rains.
Mr Lesaigor said disaster response teams evacuated about 11 people using a helicopter.
He said most of them were caught unawares when raging waters swept into their rooms and destroyed property.
"We responded quickly. Nobody was hurt," he said, adding that no deaths had been reported.
He asked the people to be on high alert and avoid walking through floodwaters.