The ongoing rains will intensify on Saturday, the weatherman has said.
This is despite global forecasts saying El Nino is ending.
The rains, which are usual for Kenya every year between March and May, reduced on Thursday and Friday after days of downpour and flooding.
Kenya Meteorological Department, in a five-day forecast, said heavy storms will return on Saturday and continue to Monday.
“Rainfall is expected to continue over several parts of the country,” said Kennedy Thiong’o, a deputy director at Met.
“Heavy rainfall events are likely to occur in some parts of the Highlands East and West of the Rift Valley, Lake Victoria Basin, Rift Valley, Southeastern lowlands, Coast and North-eastern Kenya.”
The heaviest rains will be experienced in counties near Lake Victoria and in Rift Valley highlands.
The counties are Siaya, Kisumu, Homabay, Migori, Kisii, Nyamira, Trans Nzoia, Baringo, Uasin Gishu, Elgeyo-Marakwet, Nandi, Nakuru, Narok, Kericho, Bomet, Kakamega, Vihiga, Bungoma, Busia and West Pokot.
The rest of the country is forecast to have showers over a few places in the morning and more widespread showers every evening.
This week, several meteorological organisations around the world said El Nino, which brings heavy rains in Kenya, is over.
They also predicted that La Nina, associated with long dry spells in Kenya, will take over from August.
“A transition from El Niño to neutral is likely by April-June (85 per cent chance), with the odds of La Niña developing by June-August (60 per cent),” said US National Weather Service.
The Australian Bureau of Meteorology on Tuesday declared the El Niño weather event of 2023-24 over, with odds increasing that the La Niña will return by March next year.
The bureau said predictions made towards end of the year “tend to have lower accuracy than predictions made at other times of the year. This means current forecasts … beyond July should be used with caution”.
However, the India Meteorological Department said according to their calculations, La Nina will start sometime in August or September.
While La Nina brings rain in most parts of the world, it is associated with prolonged dry weather in Kenya.
The government, on Wednesday, listed areas that are likely to experience flooding during the ongoing long rains.
Interior Cabinet Secretary Kithure Kindiki said areas along the lakes and rivers, low-laying areas and places with poor drainage are prone to flooding.
In Western Kenya, communities along lakes and rivers in HomaBay, Siaya, Busia, Nyando, Nyakach and Muhoroni are likely to experience flooding.
Other low-lying areas that risk flooding are Migori, Kakamega and Vihiga, if the quantity of daily precipitation increases beyond the prevailing levels.
Narok, Kajiado and Mombasa are also at risk of flooding.
Kindiki said hilly areas traditionally prone to mudslides include, Makueni, Nyeri, Murang’a and West Pokot counties.
He said the weather forecast for the ongoing long rains presents potential for flooding.
Urban areas with clogged or poor drainage and public or private water reservoirs across the country may also flood if the precipitation continues uninterrupted.
Kindiki said evacuation orders in some parts of the country may be issued to ensure public safety.
"The risk of significant flooding in various parts of the country has put the government on high alert. Accordingly, the public is hereby notified to exercise caution, plan their movements and avoid risky behaviour in moving waters," he said.
The CS said the government is prepared to mitigate any adverse effects of flooding in the country.
On Wednesday, the National Disaster Operations Centre at the Ministry of Interior and National Administration reconvened the Multi-Agency Disaster Management Team.
The team was established last year during El Nino rains to ensure a coordinated, whole-of-government approach to monitor and organise government response programmes.
Kindiki said the Kenya Red Cross Society and relevant national and international humanitarian agencies have been co-opted to work with the government to provide a coordinated response.
He directed the County Security and Intelligence teams to work with county governments to monitor and report situations.