Kenya is bracing for what forecasters say could be one of the stronger episodes of El Niño floods in recent years, and the government has now identified the places expected to bear the brunt. The National Disaster Operations Centre (NDOC), working under the Ministry of Interior and National Administration, has released a national risk assessment identifying 18 counties as highly vulnerable to floods, landslides, drought, disease outbreaks, and infrastructure damage in the coming rainy season.
The announcement, made in a statement released on 10 August 2026 by the Ministry of Interior and National Administration, comes as authorities prepare for El Niño weather conditions expected to begin in October 2026. If your home, farm or business sits in one of the flagged counties, here is everything you need to know.
Why the Alarm Bells Are Ringing Now
El Niño isn’t just a buzzword this year – meteorologists are treating it as a serious threat. The Kenya Meteorological Service has warned of an increased likelihood of a strong El Niño developing, with an 81–85 percent probability that the phenomenon will be strong and a 97 percent chance that its effects will persist into early 2027.
This isn’t the country’s first brush with a destructive El Niño. In the 2023/24 El Niño floods, the death toll rose steadily through the season – from 76 fatalities in late November 2023 to 120 by the end of that month, 160 by early December, and at least 174 by 20 December 2023, according to the UN Office for the Coordination of Humanitarian Affairs (OCHA), with more than half a million people displaced nationwide. Thirty-eight of Kenya’s 47 counties were affected by a combination of riverine flooding, flash floods and landslides, with roughly 90 percent of those affected concentrated in Mandera, Garissa, Tana River, Wajir, Isiolo and Meru.
That painful history is exactly why the government is moving early this time – mapping out exposure zones months before the rains are due, rather than reacting after disaster strikes.
How the Government Built the Risk Map for El Niño Floods
The NDOC’s national risk assessment didn’t happen in isolation. It draws on weather modelling, historical disaster data and vulnerability mapping to classify areas according to the type of hazard they’re most likely to face – because the floods do not affect every high-risk county the same way. Some face too much water; others face too little.
According to the assessment, the identified counties have been prioritized in response planning based on their vulnerability to various risks, and more areas may be added to the plan if experts consider them vulnerable to El Niño risks.
Authorities aren’t waiting to react once the rains arrive. The National Emergency Multi-Agency and County Emergency Response teams are already on high alert and are being sensitized on their roles in view of the expected weather situations.
Note: While the government’s operational priority list stands at 18 counties, other agencies, including FAO and WFP, project risks in up to 23 counties under their anticipatory humanitarian planning.
The Full List: 18 High-Risk Counties by Region
Coast Region
Coastal counties are staring down a mix of flooding and erosion threats. In the Coast Region, Tana River, Kilifi, Lamu, Mombasa and Kwale may experience flooding, storm surges, coastal erosion and infrastructure damage, with residents in some areas facing possible displacement by El Niño floods.
- Tana River
- Kilifi
- Lamu
- Mombasa
- Kwale
Lake Basin Region
Communities around Lake Victoria face a familiar but dangerous combination of hazards. In the Lake Basin region, Kisumu, Busia, Siaya, Homa Bay and Migori are expected to experience flooding, landslides, disease outbreaks and cases of displacement.
- Kisumu
- Busia
- Siaya
- Homa Bay
- Migori
Rift Valley Region
Here, the picture is more complicated – some areas could swing between drought and sudden flash flooding. In the Rift Valley, Turkana, Baringo, West Pokot and Narok have been identified as vulnerable to drought, flash floods, landslides, livestock losses and food insecurity.
- Turkana
- Baringo
- West Pokot
- Narok
North Eastern Region
For pastoralist communities in the north, the bigger concern is a lack of water rather than too much of it. The North Eastern counties of Garissa, Wajir and Mandera could face drought, water shortages, poor pasture conditions, food insecurity and potential livestock losses.
- Garissa
- Wajir
- Mandera
High-Risk Urban Centres
It’s not just rural and pastoral counties on the list – Kenya’s biggest cities are exposed too. Beyond rural counties, the assessment identifies Nairobi, Mombasa and Kisumu as high-risk urban centres, facing the prospect of urban flooding, overwhelmed drainage systems, strain on public infrastructure and disruption to essential services.
- Nairobi
- Mombasa
- Kisumu
Note: Mombasa and Kisumu appear both as regional counties and as flagged urban centres, given their dual exposure to coastal/lake flooding and urban infrastructure strain.
Quick-Check: Is Your County on the List?
- 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 centres: Nairobi, Mombasa, Kisumu
A Repeat of History? Tana River and Garissa Under Watch Again
Two counties stand out for the wrong reasons. Tana River and Garissa, among the hardest-hit counties during the 2023/24 El Niño season, are on both risk lists again this season. That repetition underscores just how exposed these areas remain to Kenya’s cyclical weather extremes – and why disaster response agencies are treating them as priority zones for pre-positioned resources.
In fact, the government’s current plan to pre-position boats in flood-prone areas echoes a similar pledge Nairobi County made ahead of the 2023/24 El Niño season, suggesting lessons from the past are shaping this year’s preparedness strategy.
Livestock in the Crosshairs: KVA Sounds the Alarm
Beyond El Niño floods and displacement, Kenya’s livestock economy – the backbone of livelihoods for millions of pastoralists – is facing its own distinct threat. The Kenya Veterinary Association (KVA) has issued a stark warning about what an intensifying El Niño could mean for animal health and farmer incomes.
KVA President Dr Kelvin Osore said the anticipated weather patterns could increase livestock disease outbreaks, deaths and injuries while disrupting livestock markets and damaging critical infrastructure. Osore noted that climate agencies have forecast a high probability of El Niño conditions developing and persisting through the remainder of 2026 into early 2027, posing significant risks to Kenya’s livestock sector and the livelihoods of millions of pastoralists and livestock farmers.
The risks aren’t limited to flooding alone. The association said pastoralists and livestock farmers remain particularly vulnerable to flooding, contaminated water sources, disease outbreaks and disruptions to feed and livestock value chains.
KVA’s Recommendations for Livestock Owners
The veterinary body is pushing for emergency pre-emptive vaccination campaigns and has laid out practical steps farmers can take now, before the rains set in. KVA has urged livestock owners to consult veterinary professionals, strengthen vector and parasite control, protect feed and water supplies, identify safe areas ahead of possible flooding, and promptly report unusual animal illnesses or deaths.
- Consult veterinary professionals early rather than waiting for symptoms to appear
- Strengthen vector and parasite control measures on farms
- Protect feed and water supplies from contamination
- Identify safe, elevated ground in advance of potential flooding
- Report unusual animal illnesses or deaths promptly to authorities
The association also called on the government to activate emergency destocking by September 2026 and deploy mobile veterinary units to high-risk pastoral areas.
The association pointed to lessons from the 2023–2024 El Niño, which triggered widespread flooding, displacement, infrastructure destruction and livestock losses, as proof of the need to invest in preparedness before extreme weather strikes. As Osore put it plainly: “Preparedness is considerably less costly than emergency response after disasters have already occurred.”
What Experts Say About Preparedness
International agencies are backing Kenya’s early-warning approach. A joint assessment from the FAO and WFP has laid out a clear preparedness roadmap, and the warnings go beyond flooding alone. The agencies warn that climate change is raising the likelihood and severity of El Niño-related hazards, including flash floods, outbreaks of water-borne disease, soil erosion, crop destruction and livestock losses – which may later be followed by prolonged dry spells, extreme heat and an increased risk of cardiovascular, respiratory and maternal and child health problems.
On the response side, the joint FAO–WFP report recommends clearing drainage systems, activating flood preparedness protocols, relocating people in high-risk areas, strengthening flash flood early warning systems, improving urban drainage, expanding mobile healthcare and promoting agricultural, health and property insurance.
Insurance and financing are also being highlighted as critical safety nets. FAO resilience specialist Dominique Reumkens stressed the need to protect people’s lives, property, livestock and crops, noting that where losses occur, blended financing solutions, including insurance, are critical. Reumkens further argued that improved forecasting, timely early warnings, pre-arranged financing and wider insurance coverage would reduce disaster losses and speed recovery.
What Happens Next
The 18-county list is not necessarily final. Both the NDOC and Interior Ministry have signalled that the risk map will be updated as conditions evolve. The government said the counties have been prioritised according to their vulnerability to the different risks associated with the expected weather conditions, and the list is not considered final, with the Ministry noting that more areas may be included in the plan if experts consider them vulnerable to El Niño risks.
Interior CS Murkomen said the government will continue monitoring weather updates and field conditions and will be ready to expand the list of priority counties if assessments indicate additional risks.
How to Stay Safe If You Live in a High-Risk County
Whether you’re in a flood-prone coastal county, a drought-exposed pastoral area, or one of the three flagged cities, preparedness now can make a real difference later. Consider the following steps:
- Follow official updates from the Kenya Meteorological Service and your County Emergency Response team
- Clear drainage around your home or business ahead of the October–November–December rains
- Identify an evacuation route and a safe, elevated location if you’re in a flood-risk zone
- Store clean water and non-perishable food in case of disruption to supplies
- Protect livestock by securing feed, water sources and vaccination records, and knowing where to move animals if flooding threatens
- Report unusual weather damage or animal illness to local authorities promptly so response teams can act quickly
The Bottom Line
Kenya’s 18 flagged counties span nearly every region of the country – from coastal floodplains to drought-stricken pastoral lands to the capital city itself. With forecasters warning of a potentially strong El Niño stretching into 2027, and painful memories of the 2023/24 season still fresh, the government’s early mapping exercise is as much about avoiding repeated tragedy as it is about logistics. If you live, farm or do business in any of the counties listed above, now is the time to prepare – not after the first floodwaters rise.
Frequently Asked Questions (FAQs)
1. Which counties are on the El Niño high-risk list?
The government has flagged 18 counties across four regions, plus three high-risk urban centres:
- 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 centres: Nairobi, Mombasa, Kisumu
Mombasa and Kisumu appear in both their regional lists and the urban centres list due to dual exposure to flooding and infrastructure strain.
2. When is El Niño expected to hit Kenya and how strong will it be?
El Niño effects are expected to begin around October 2026 and persist into early 2027. Forecasters estimate an 81–85% probability that this year’s El Niño will be strong, with a 97% chance that its impacts will continue into early next year.
3. What hazards should residents in high-risk counties prepare for?
Hazards vary by region:
- Coastal counties: Flooding, storm surges, coastal erosion, infrastructure damage, possible displacement
- Lake Basin counties: Flooding, landslides, disease outbreaks, displacement
- Rift Valley counties: Drought, flash floods, landslides, livestock losses, food insecurity
- North Eastern counties: Drought, water shortages, poor pasture, livestock losses, food insecurity
- Urban centres (Nairobi, Mombasa, Kisumu): Urban flooding, overwhelmed drainage, infrastructure strain, service disruptions
4. What is the Kenya Veterinary Association (KVA) advising livestock owners to do?
KVA President Dr Kelvin Osore has warned of increased livestock disease outbreaks, deaths and infrastructure damage. The association recommends:
- Consulting veterinary professionals early (before symptoms appear)
- Strengthening vector and parasite control on farms
- Protecting feed and water supplies from contamination
- Identifying safe, elevated ground in advance of flooding
- Reporting unusual animal illnesses or deaths promptly
KVA has also called for emergency pre-emptive vaccination campaigns, emergency destocking by September 2026, and deployment of mobile veterinary units to high-risk pastoral areas.
5. Is the 18-county list final or can more counties be added?
The 18-county list is not final. Both the NDOC and the Ministry of Interior have stated that the risk map will be updated as conditions evolve. More areas may be added if experts determine they are vulnerable to El Niño-related risks.
Note: While the government’s operational priority list is 18 counties, other agencies such as FAO and WFP project risks in up to 23 counties under their anticipatory humanitarian planning.
References:
- KBC – El Niño: Government maps out high-risk counties
- Kahawatungu – Government maps out 18 high-risk counties ahead of expected El Niño
- Tuko.co.ke – Govt Identifies 18 Counties at High Risk of El Niño, Warns of Potential Flooding
- The Kenya Times – Murkomen Maps 18 Counties Facing High Risk Of El Niño Rains In October
- NTV Kenya – El Niño: 17 counties flagged as high risk
- Daily Nation – El Niño: 18 counties flagged as high risk
- Pulse Kenya – Kenya Flags 18 Counties Over High El Niño Disaster Risk
- Nairobi Wire – Government Puts 18 Counties on High Alert as Kenya Braces for Strong El Niño
- Capital FM Kenya – Govt maps 18 high-risk counties ahead of October El Niño rains
- The Star – El Niño alert: KVA warns of livestock losses, calls for urgent preparations
- Capital FM Kenya – Vets warn El Niño could hit livestock sector hard
