List of High-Risk El Niño Counties As Health Ministry Rolls Out Preparedness Plan

The Ministry of Health has launched an El Niño preparedness plan covering 18 counties classified as high-risk, as the country gears up for another round of heavy rains and the health fallout that tends to come with them.

Public Health and Professional Standards Principal Secretary Mary Muthoni says the ministry is now leaning on health partners to help shore up readiness efforts and soften the blow of the rains expected later this year.

She made the remarks on Wednesday during a health partners’ engagement session focused on planning for the Kenya Public Health International Conference (KEPHIC) 2026, stressing that no single actor can handle the response alone.

“We have experienced El Niño before, and we have taken time to learn from past disasters and build on the challenges we faced so that we can better mitigate its effects,” Muthoni told partners at the meeting.

Kenya’s last major brush with El Niño came in 2023, when 43 counties were affected, leaving communities to contend with flooding, disease outbreaks and disruptions to basic services. That experience appears to be shaping much of the current planning.

The Interior Ministry, for its part, has already named its own list of 18 high-risk counties in anticipation of the 2026 rains, cautioning that floods, disease outbreaks and food shortages are all real possibilities.

Nairobi made the cut, with officials pointing to urban flooding, clogged drainage systems and infrastructure that’s already under strain even before the rains arrive

Along the coast, Tana River, Kilifi, Lamu, Mombasa and Kwale have been flagged over concerns about heavy downpours and rising sea levels, a combination expected to bring flooding, storm surges, erosion, infrastructure damage and, in some cases, displacement.

The Lake Basin region isn’t being spared either. Kisumu, Busia, Siaya, Homa Bay and Migori are all being closely monitored, with the Interior Ministry warning of a familiar mix in that region: flooding, landslides, disease outbreaks, waterborne illnesses and the possibility of families being forced from their homes.

To get ahead of it, the Ministry of Health is now calling on partners to help with temporary medical facilities, emergency medical services, health promotion campaigns, nutritional assessments, safe water and sanitation efforts, logistics support, and protection of critical infrastructure and medical supplies in the affected areas.

One of the bigger disease-prevention measures on the table: the ministry plans to roll out 10 million treated mosquito nets starting in November, targeting more than four million Kenyans expected to be affected by the rains across the country.

Separately, Muthoni revealed that the State Department for Public Health has drafted a Cabinet memorandum proposing a monthly national cleanliness day.

“We are proposing that we set aside one day every month for Kenyans to clean their estates and surroundings, similar to the programme in Rwanda,” she said.

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