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Overnight, 11 people were rescued after a minibus taxi, known locally as a matatu, got stuck as water rose in the capital Nairobi, according to the Kenya Red Cross, while two children were saved from a flooded house.
The heavy rainfall over the past week has triggered flash floods not seen in years. Rivers have burst their banks, flooding homes and damaging roads, power- and water- lines.
Some roads have been closed after bridges were damaged in Nairobi, while some schools were also flooded after Saturday's downpour.
The Interior Ministry warned on Sunday that different parts of the country were continuing to experience heavy rains, increasing the risk of flooding.
The authorities have urged residents in low-lying areas to move to safer ground and more than 2,000 people have had to leave their homes to seek shelter.
Police say that search and rescue operations are continuing following the "torrential rain and subsequent devastating flooding affecting various parts of the country".
More than half of those killed - 33 - have been in Nairobi, where poor drainage has been a major factor, along with the obstruction of rivers caused by unregulated development.
President William Ruto on Sunday said that emergency food supplies and medical assistance were being delivered to those affected.He also said that the authorities were clearing blocked drainage systems.The flooding has not just affected Kenya.
More than 100 people have been killed in neighbouring Ethiopia following floods and landslides in the south of the country.Many factors contribute to flooding, but a warming atmosphere caused by climate change makes extreme rainfall more likely.
The world has already warmed by about 1.1C since the industrial era began and temperatures will keep rising unless governments around the world make steep cuts to emissions.