The Interior Ministry has classified 18 counties as high-risk for flooding as Kenya heads into the October-December short rains, with the National Disaster Operations Centre warning that El Niño conditions could overwhelm urban drainage and force evacuations in low-lying and riparian areas. The government has rolled out a seven-point contingency plan, and the Kenya Red Cross says as many as 2 million people could be affected nationwide.
As of September 2026, the short rains have not yet begun in most of the country, but forecasters expect an early onset in parts of Western, Nyanza and North Eastern Kenya, giving county governments and residents in the highest-risk areas a narrow window to prepare.
Which 18 counties are flagged as high-risk?
The Interior Ministry and NDOC grouped the high-risk counties by region, citing exposure to heavy rains, rising river levels or, in some cases, a difficult mix of both drought and flooding threats:
- Coast: Tana River, Kilifi, Lamu, Mombasa, Kwale
- Lake Basin: Kisumu, Busia, Siaya, Homa Bay, Migori
- Rift Valley: Turkana, Baringo, West Pokot, Narok
- North Eastern: Garissa, Wajir, Mandera
- Urban centre: Nairobi, flagged separately for blocked drainage and strained infrastructure rather than river flooding
Nairobi’s own mapping exercise has since gone further than the national list: City Hall has identified 246 flood hotspots across the capital and estimates roughly 25,000 households live in areas at risk, according to county officials cited by the Eastleigh Voice.
Why Nairobi, Kisumu and Mombasa specifically?
All three are named repeatedly in government briefings because they combine two risk factors at once: they sit on or near rivers and low-lying drainage basins, and they carry the country’s largest urban populations, meaning a blocked culvert or a silted channel puts far more people and property in the path of water than the same failure would in a rural county.
What is the government’s seven-point plan?
Under a National Contingency Plan drawn up with county governments, humanitarian partners and security agencies, authorities say they are moving on seven fronts before the rains intensify:
- Hotspot mapping — identifying flood-prone riverine, coastal, landslide-prone and low-lying zones county by county.
- Drainage and desilting — the Kenya Urban Roads Authority and county teams are unclogging culverts and water channels at identified choke points.
- Pre-positioned emergency supplies — relief items and response teams placed on standby for search, rescue and evacuation.
- Evacuation centres — temporary holding grounds identified for people living on riparian land or in other high-risk zones.
- Water-level monitoring — closer tracking of rivers and dams, particularly where communities live along the banks.
- Infrastructure inspection — bridges, roads and utilities in flood-prone areas being checked for vulnerabilities.
- Community early-warning systems — strengthened through chiefs, assistant chiefs and Nyumba Kumi structures so alerts reach villages and estates directly.
In Nyando, one of the areas hit hardest by flooding in past rainy seasons, county officials say about 10 evacuation centres are already stocked with food, non-food items, medical supplies, mosquito nets and drugs for waterborne diseases.
How many people could be affected?
The Kenya Red Cross Society’s disaster risk reduction team estimates that up to 2 million people could be affected by this year’s El Niño rains nationally, a figure that spans direct flood damage, displacement and secondary effects such as waterborne disease outbreaks and disrupted access to markets and schools. That number is broader than the 18-county high-risk list, since it also accounts for communities in medium-risk zones who could still face localised flooding, landslides or road cutoffs.
Is this the same as the drought Kenya has been dealing with in 2026?
Not quite the same event, but part of the same climate pattern. As 254.ke reported in August, Kenya’s meteorologists linked this year’s dry spell and the flood risk now facing the country to the same evolving El Niño and a positive Indian Ocean Dipole — a combination that raises the odds of both drought and flooding in different parts of the country within the same year. Nairobi has already had a preview of what that can look like: heavy rains earlier this year flooded city streets and disrupted transport after a single intense downpour overwhelmed drainage.
What should residents in high-risk areas do now?
- Check with your county government or local chief’s office on whether your specific area has been mapped as a flood hotspot.
- Avoid building or staying on riparian land — land within the legally protected buffer along a riverbank — even temporarily.
- Keep an emergency bag ready with identification documents, medication and a torch if you live in a mapped high-risk zone.
- Follow county-level updates rather than relying only on national bulletins, since evacuation orders in past seasons have been issued area by area, not nationwide at once.
- Report blocked drains or culverts near your home to your county public works office rather than waiting for the rains to expose the problem.
FAQ
When will the El Niño rains start in Kenya?
The Kenya Meteorological Department has forecast an early onset in parts of Western, Nyanza and North Eastern Kenya, with the main October-December short rains season affecting the rest of the country through the final quarter of 2026. The same climate pattern is also expected to strain public finances — Kenya’s own climate adaptation planning has previously put the country’s overall adaptation funding need at Sh2.2 trillion by 2035.
Which counties are most at risk of flooding?
The Interior Ministry’s high-risk list names 18 counties: Tana River, Kilifi, Lamu, Mombasa, Kwale, Kisumu, Busia, Siaya, Homa Bay, Migori, Turkana, Baringo, West Pokot, Narok, Garissa, Wajir, Mandera and Nairobi.
Is Nairobi really at flood risk?
Yes. City Hall has mapped 246 flood-prone hotspots across Nairobi and estimates about 25,000 households sit in at-risk areas, largely due to blocked drainage and construction on riparian land.
What is the government doing to prepare?
A seven-point National Contingency Plan covers hotspot mapping, drainage desilting, pre-positioned emergency supplies, evacuation centres, water-level monitoring, infrastructure inspection and community-level early warning through chiefs and Nyumba Kumi structures.
How many people could be affected this year?
The Kenya Red Cross estimates up to 2 million people nationally could be affected by flooding, displacement or related health risks during this El Niño season.
By the 254.ke Newsroom
