The MET has issued a heavy rains alert starting Thursday, to last until Monday.
The heavy rain will be accompanied by strong winds.
High rainfall intensity is expected over Northeastern, Central and Coast.
Counties highlighted in the alert include Kakamega, Vihiga, Nandi, Elgeyo Marakwet, West Pokot and Trans Nzoia. Others are Nakuru, Narok, Laikipia, Baringo and Nyeri.
Residents in Nairobi, Mombasa, Kilifi, Kwale, Tana River and Lamu are also advised to be on the lookout for potential flash floods.
"Flood waters may suddenly appear even in places where it has not rained heavily and can be deeper and faster than they look," said the statement from the Kenya Meteorological Department.
Residents are advised to avoid driving through, or walking in moving water or open fields and against seeking shelter under trees.
The advisory urged residents to stay away from grilled windows and to minimise exposure to lightning strikes.
People in landslide-prone areas have also been advised to be on high alert.
"The heavy rains and moderate to strong winds may result in storm surges along the coast."
The warning comes shortly after four people died following a heavy downpour in Meru County on Wednesday evening.
Three bodies were recovered in Buuri sub-county yesterday while the fourth body was found in Karegeria village in Imenti North.
Residents of Gitimene in Naari found the bodies of two men and a woman that had been swept 400 metres from a building they had been sheltering in at Gitimene shopping centre.
Two of the victims were identified as Boniface Muriungi, 15, who was studying at Miugune Vocational Training Centre, and James Karani aged 25.
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