Government Names 18 High-Risk Counties Ahead Of Expected El Niño Rains

The Interior Ministry has put 18 counties on high alert as El Niño rains loom over Kenya in 2026, with officials warning of floods, disease outbreaks and food shortages once the wet season sets in.

A notice released on August 10 puts Nairobi and its surrounding areas near the top of the list. According to the ministry, urban flooding, blocked drainage systems and strained infrastructure are the capital’s biggest vulnerabilities as the rains approach.

Along the coast, Tana River, Kilifi, Lamu, Mombasa and Kwale have also been flagged, given how exposed the region is to both heavy rainfall and rising sea levels. Officials expect these counties to contend with flooding, storm surges, coastal erosion, infrastructure damage and, in some cases, displacement once the rains intensify.

The Lake Basin region isn’t spared either. Kisumu, Busia, Siaya, Homa Bay and Migori are all under close watch as the season approaches, with the ministry warning of a mix of flooding, landslides, disease outbreaks, waterborne illnesses and possible displacement of families.

Nairobi, Mombasa and Kisumu have also been grouped separately as major urban centres likely to feel similar strain, particularly from blocked drainage systems disrupting daily life. The ministry expects these three cities to bear the brunt of service disruptions and infrastructure pressure once the rains peak in the coming months.

Then there’s the other side of the coin: counties already battling drought. Turkana, Baringo, West Pokot and Narok in the Rift Valley face an unusual double threat: drought and flooding at the same time. For these largely pastoral communities, the concern is livestock losses, landslides and worsening food insecurity.

Garissa, Wajir and Mandera round out the list. Drought, water scarcity and poor pasture are already straining livelihoods in these North Eastern counties, even before the rains arrive.

Beyond the immediate flood risk, there’s a quieter danger building. In a statement released the same day, the IGAD Climate Prediction and Applications Centre (ICPAC) warned that the wider East African region could also be looking at a resurgence of Rift Valley Fever (RVF).

Kenya is expected to face the highest risk in the region. El Niño-driven floods tend to create ideal breeding conditions for mosquitoes, which in turn accelerates the spread of the virus among livestock, and eventually, to people.

The knock-on effects hit human health, food security and livelihoods all at once. The danger isn’t confined to Kenya, though. ICPAC’s warning extends across Burundi, Ethiopia, Rwanda, Somalia, South Sudan, Uganda and Tanzania, where regional flooding and cross-border livestock movement could make outbreaks even harder to contain.

“These forecasted climate conditions are expected to create favourable ecological conditions for Rift Valley fever (RVF) transmission. This poses an imminent danger to the countries including Burundi, Ethiopia, Kenya, Rwanda, Somalia, South Sudan, Uganda, and the United Republic of Tanzania,” ICPAC said in the statement.

The centre cautioned that without coordinated early warning systems and a fast regional response, outbreaks could devastate livestock herds, disrupt trade, and push already vulnerable communities deeper into poverty.

Heavy rains, it added, will likely make matters worse by damaging roads and infrastructure, cutting off access for emergency aid just when it’s needed most.

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